Does yours have a switch on the back near the power inlet that lets you decide which kind of footswitch you are going to use? If so, make sure it is set to the correct option.
The only switching problem I have encountered was the system trying to turn on every channel/mode at the same time, and I fixed it by accidentally shorting two pins in the footswitch jack (I was trying to clean dust out of the jack with the screwdriver while it was turned on, and it arced). Mine is a MIDI quad with FU-2A.
Roadster, Mark IV, Traditional/ Stiletto 412
Gone: Quad MIDI Pre, TriAxis V1 & V2, Formula Pre, Simul-Class 2:NINETY, 20/20 Stereo
Great deals with: Prestige20, DMTransmutation, PaxMan, Forty6and2, jdurso
WTB: Modded MTS modules