Check to see if you have 'Registration Sequence' turned on by pressing 'MENU' > 'Regist. Sequence'.
If the 'Sequence' button on this page is turned on, any pedals that are assigned to 'Regist+' and 'Regist-' will carry out these functions rather than their defaults or what you have assigned to them.
If it is turned on, simply turn 'Sequence' off and see if this restores 'normal' functionality.
Regards
Ian