I have had similar problems. I have had my TF for only a couple of weeks, so it may well be my lack of knowledge of the device, but in the last couple of days I have had a problem similar to plinky, both in bank mode and play mode.
In bank 1:1, I have saved a vintage delay patch with only one delay (A) and the ex pedal assigned only for the dry/wet mix. After playing for a few minutes, the sound has a modulation/chorus added which I can turn off by returning the modulation depth control to 0 but then it will soon re-appear again. I have checked, and as far as I can tell the ex p is only assigned to the control for the wet/dry miix
I am still trying to suss this out myself, but any comments that may help would be much appreciated.