Hi.
Make sure that you are using an insert y-cable (1TRS- 2 TS). I have a Dunlop mini x as EXP 1 for wah and an Ernie Ball tap tempo switch as FS 5 for solo boost working perfectly this way. If you are using the correct cable, then it is probably a setting somewhere that is not correct. I am using it mostly in stomp mode using a Tech 21 midi mongoose for program changes. Will probably switch to snapshot mode once I get comfortable with it.