Does it happen if you have a buffered pedal in front? High-impedance signals (e.g. direct from passive guitar) are much, much more susceptible to picking up LFO noise, and it almost always happens on the input since most of the internals and the output signal coming from the pedal are low impedance and therefore better able to reject that type of noise.
I've found that many/most instances of ticking will go away if the input signal has been buffered in advance - which is going to be the normal real-world use case most of the time, but not usually done when testing a build.
I've found that many/most instances of ticking will go away if the input signal has been buffered in advance - which is going to be the normal real-world use case most of the time, but not usually done when testing a build.