I'm using an FS300, which I believe is basically the same pedal with a different color scheme, and I haven't had any problems. I don't recall hearing of anyone with similar problems with the FS3X, but that doesn't mean there haven't been.
Since the FS3X isn't powered (no batteries, no lights, no external power), it wouldn't be my first guess in a hunt for a ground loop, but that's what it sounds like. Here are a couple of questions that might help us narrow down where the problem is and then find a solution…
How do you have the FS3X hooked up (type of cable and what connections)?
What else is hooked up to your TF (guitar, amp, other pedals (mono/stereo), power supply, MIDI, expression pedal, USB)?
Are you using the Eventide power supply?
What do you have the aux switches assigned to?
What are the input and output level switches set to?
Are the TF and the FS3X attached to a pedalboard?
If so, what else is on that pedal board (including pedals, power supplies, cables, etc)?
If you are using a pedal board, does the "click" still occur when you remove the TF and FS3X from the pedal board?
Maybe more importantly, does the "click" go away if you use a different cable to attach the FS3X?
Is the click still there when you use the switches on the TF to control the same functions?
Is the click still there when you use a different guitar and/or a different amp?
Basically, the more details you can provide about your entire rig, the easier it will be to help you determine why this is happening? It's really just a matter of troubleshooting in order to isolate the problem, to determine precisely what is causing the "click." Then, we can help you find an answer.
