Hmmm...
Bear with me, and don't take any of this personally. I'm going to make some observations about the general misconceptions about circuitry that guitarists employ. If you or anyone else reading can be offended, please read again and simply realize that I'm just trying to help, and you should look at the message here.
Alrighty. I think you're misunderstanding the purpose of buffer somewhat. This is causing a lot of problems for people on TGP and HC, so you're not alone. I explain this stuff to people a couple times a week it feels like. Perhaps this will help:
Your guitar signal is a high impedance signal. This is great, and it's simply a part of how your pickups operate. However, what this does is 'loads' the cable you're running. This often doesn't matter, however if you run a loooong cable to your amp (think 35+ feet) you're going to experience what many describe as a 'loss of clarity' or 'a loss of high end.' It's a lot like filling up a tub with water, then unplugging it. It's going to drain slowly. Your drain pipe can't really handle all of the water and you don't get a clear easy 'flow' going.
If you run a 20' cable from your amp to your pedalboard, and you have about 10' of cables between all your pedals, and then run even a 10' cable to your guitar you could experience some of this perceived 'tone loss.' This is why many pedals, like the popular Boss type pedals all have buffered bypass. What will help the situation is to turn that high impedance signal into a low impedance signal.
This is the key to the issue - what a buffer does is takes your high impedance signal and transforms it into a low impedance signal - this is like taking that tub of water, and instead of filling it, you just turn the water on at a rate that it will nicely flow down the drain and never actually fill the tub, water going down the drain at the same rate as it enters the tub. A good buffer close to your guitar will relieve the 'loading' of your cable, and it will flow nicely down to your amp, making it seem like your guitar cable is only 10' instead of the 40' you may be using with a pedalboard.
Recently, it started becoming popular to use true bypass pedals. Since 3PDTs are so cheap and common now it's really easy to make up a pedal board full of True Bypass pedals if you like DIY. This is a great thing, because part of the side effect of all those buffers interacting with each other can be a negative accumulation of unnecessary circuitry which could affect your guitar signal. In fact, many people started doing bypass mods to some of their buffered pedal because the idea got out there that 'True Bypass is better.' Since piling buffers together seemed to be bad, True Bypassing EVERYTHING seemed to be answering the problem. What's happened in the end is that some people report that there seems to be more and more clarity and less and less 'mud' when they start using true bypass switches, so that info made people want to try and build entire pedal boards with true bypass pedals - can't have too much of a good thing right?
What happened when these guys started building pedalboards with true bypass pedals was that they started reporting that when they plugged straight into their amp with a 10 foot cord instead of their pedalboard it was 'like taking a blanket off their amp.' All of the sudden people realized that while True Bypassing some pedals was really great, there was a problem because in some cases people were running 30, 40, 50 or even 60 feet of cord between their guitar and amp - this was causing MAJOR 'tone loss.' Obviously a bad thing right?
So what was the answer? Strategic buffering using discrete and low interference buffers. Many recommend using buffers in two places - as soon as you can in your signal chain (right after your guitar) and/or one at the end of your pedal board going to your amp. I will say that there are specific reasons for these two places.
Having a buffer at the front of your pedalboard will allow your signal to be changed from high to low impedance as soon as it is possible. This means that if you use a 10' cord to your pedalboard, in theory this would act just like you were using a 10' cord right into your amp. This gives you as little 'tone loss' as you can experience while still moving around with your guitar. You can use longer cords, but getting up to or over 30' may not be wise.
Having a buffer at the end of your pedal chain MAY OR MAY NOT be necessary. What it depends on is the OUTPUT IMPEDANCE OF THE LAST PEDAL IN YOUR CHAIN. Many amps expect a very specific impedance. For example, most Fender amps I know of have a 1M input resistor, giving it a 1M input impedance. However, if your last pedals has a 470K input impedance they obviously do not match. The idea here is that all of a sudden you've slightly changed the hole in your tub of water, and now water is backing up in your tub a little bit and causing some 'tone loss.' I'm not sure I buy this, but experimentation with this theory may help some out. What I suggest is if you're considering doing this, look up the input impedance of your last pedal, and then see if it matches your amps. If it does, you're likely fine. (I will say that I may have that wrong. In any case, I don't really buy into it and mostly just think that one buffer early on is the answer to an impedance problem)
So what does all this mean? There's a common misconception of what Buffers do out there. People talk about NEEDING a good buffer from T1M or like the Klon one, or whatever. That is frankly a load of malarky. Most people do NOT need a buffer. What they do need to do is understand a little bit better what Buffers ACTUALLY do, then see if they actually need to change their impedance. That's all buffers are for. Tone shaping using eq is likely what most people expect out of a Buffer, but that's actually a different circuit function that is outside the range of most buffer circuits. That said, some buffers are reported to 'change your tone' or have an amount of 'effect'. I suspect this is a hysterical response, simply because people are expect to hear something so they do.
I will also note that THERE ARE BADLY DESIGNED BUFFERS. The Whammy pedal is famous for it, as are many DOD and other 80's and 90's era pedals. Sometimes these are myths, and in some cases it is simply because they haven't been designed properly. They are often designed instead to provide silent or easy or cheap switching, but pedal builders have learned a lot from the 'hard bypass' type pedals that honestly do 'suck tone' by shunting your signal to the wrong places.
The only test you need to do is to take your cord you usually plug into your pedalboard, then plug straight into your amp. Now plug back into your pedalboard and turn ALL your pedals off. Does it sound the same? You're find and you don't need a buffer. IF it does sound like junk, you may benefit from ONE good buffer at the beginning of your chain, and/or the removal of another pedal later on in the chain. You can test which it is by first removing your 'buffered' pedals from your chain one at a time. If all of the sudden your signal gets better by removing one or more of these pedals, put them in True Bypass loops or mod them or remove them from your board. IF however it's because of how long your chain is, or because you use all true bypass pedals, it's likely a buffer at the beginning of your circuit is needed. Build one and see, there are LOTS of examples of them, including the one in the DIY page of my website (signature below).
Last but not least about buffers is that MOST effects naturally change your pedals impedance. No joke, you may not need a buffer. I don't use one despite having almost all true bypass pedals on my pedal boards. Why? simply because I ALWAYS leave my compressor on. I don't even know why I build them with switches. Because they're first in line, I have absolutely no need to build a 'buffer' and throw it in my chain, the comp does it for me.
Ok. That's settled I hope. Feel free to correct or help me anyone who gets this better than me. I'm doing my best.
On to the REAL help for you man.
Nobody has told you yet hey? Fuzzes don't like buffers. It's weird. Same reason they don't like Wah pedals either. It has to do with the way that impedance is done in pedals that use Ge transistors. You just gotta adjust the chain so that the fuzzes 'see' your guitar before a buffer. Move it up in your chain or get rid of the fuzz is your only real options to solve your problem. Putting a buffer into your pedal is actually going to be detremental and not helpful in the least.
THERE ARE some fuzzes that work well with Buffers, so be aware that this may or may not apply to you. Usually if you're using Silicon fuzzes you're good to go.
Next, the 'headroom' issue. Headroom is also a misunderstood idea, and most people never approach the headroom they are offered in their effects, especially buffers. Headroom is the 'leniency' a circuit has to the power you feed it with your signal. Essentially, the easist way to describe it is that your signal has a certain power. If your guitar signal were to 'hit' the pressure bladder at the fair with a sledgehammer, you have run out of headroom when the bell is rung at the top. The only circumstances this really happens in is if you use very high powered pickups like EMGs or Duncan Distortions or the like. However, many of those active pickups actually lower the impedance using circuitry in the guitar itself before heading down your patch cord, so in some cases you don't even need to worry about it!
So, when you feed your buffer ~18V, yes you raise your headroom. However, if you signal never gets to higher than a '5' on your headroom scale, then raising your headroom from 10 to 20 doesn't really do anything for you. You probably don't need more headroom at all, and it's sorta a useless gesture.
On to your fade ins. I suspect it has more to do with the caps in the pedals charging or releasing in strange ways which is indicitive of other problems I would need more information about to really help with. If it only matters when these fuzzes are whacked out on buffers, you should know how to solve that problem now.
Dang, I think my wife is going to be mad, because I told here I'd go to bed after checking the forum. Then I wrote all this. At least I get to watch Vader and Obi duel cause I turned on A New Hope while I was typing.
Uh oh. Vader just made Obi disappear and Luke lost it. Night all.
Jacob