If you cannot test each pedal alone, and you cannot get the board into "fail mode", perhaps wiggling each cable could be a good starting point. Listen for any crackles or pops or any other abnormal behavior.
Try repeatedly activating/bypassing a single pedal at a time on each of the true bypass pedals. It could be a failing mechanical switch on one pedal.
Let us know what you find.
You will either find something interesting, or you won't.
Intermittent problems are always difficult to chase down and certainly my least favorite, however you should not dismiss a potentially valuable test just because you cannot reliably trigger the problem or because you have guessed the results. In the end, either of the above tests will likely lead you to running through each pedal anyway.
I hope that helps!