Reply to Kontrol S2 Deck with flanger glitch?

I recently started experiencing a problem with my Kontrol S2 left deck with a permanent flanger while in scratch mode. I am using the DJTT 4 deck gain=gain mapping and also the FX squared mapping for the Midi Fighter Spectra. The right deck is fine, but the left deck has a flanger effect which makes it hard to cue. I've re-installed the default S2 mapping and tried without the Midi Fighter mapping but to no avail. I have no idea how to fix this problem and it makes it impossible to practice scratching. Any ideas?