I have the same pedal, make sure the knob on the side, if looking straght at it, is turned all the way to the left. I have never had an issue with this not working for setting the unit.
NOW , I am having an issue with deleting them. I'll move the pedal so the light on TF blinks then put it in heel down position and set the param, let's say MIX, to 0 the move the pedal to toe down position and also set to 0 wait for the light to stop blinking on the TF and sometimes it works, sometimes it does nothing and sometimes it will change the low and high values of the pedal to something totally different, instead of anything near 0. Say they were at 30 and 100 and I zero it out as described above, the unit might reset them to 48 and 72 or something! I've tried to also set both heel down and toe down to 50, 100, 25, 70 etc… it just seems to work sometimes and not others, the Boss FV500 is set correct, works on setting new param changes and moves the values correctly for anything that is set….not sure what the deal is, maybe I'll make a second post for this.