a few possibilities come to mind

to be certain its not the audya run the checksum tests in the sticky topics.

if your using registrations that use octave changes and your holding notes whist changing the registration it is possible a note could hang as the audya is receiving note on data but not note off. to see if thats the case, change back to the previous registration and replay the notes. (or use the MIDI RESET function (slow and fast leslie tabs together)

check your midi channels and turn off everything that you do not need.

swap your midi cable.