I think that most of your problems arise from using the 3rd button of the AUX switch for the more sensitive functions.
What happens is that the unit reads switch A and then reads switch B, and if they are both down, views it as switch C. If you hit the switch between the point where it reads A and reads B, it will view it first as switch B, and then, when it reads the switches again, will realize its mistake and call it C. This means that from time to time, when you hit C, you will instead get B.
There's no real way round this – we could delay the readings until we have a more stable result, but this might slow down operation unacceptably. That said, this is not usually a problem, so it is possible that I have it wrong. You could try reassigning the switches and see if it makes a difference.
Further, if you assign a switch to 2 functions, you will get the 2 functions you ask for. The unit is not going to try and decide whether you want (in this case) TAP or OCTAVE, both of which may be appropriate in LOOPER mode,
If you need this extensive use of foot switches, you might want to consider a MIDI approach – this would be a way to get around the limitations of the AUX switch.
