Now I pick up your problem. But, itís not a problem of flute organ. It happens with any of Left, R1 and R2 voices. If you try e.g. press and hold the R1 part and change the regist, you will get the same behavior.
For me it is not a bug as I think that I understand how the keyboard works:
The keys of the keyboard act as a MIDI injector. When we press a key, we send several messages to the processor, Note ON, pitch, velocity... and when we release the key, we send the message Note OFF. So, if while pressing a key (note ON was sent) we change the regist, the keyboard can not change some parameters because it has not yet received the Note OFF. So, it continue playing the precedent voice we are yet playing. Itís missing the note OFF message for that key, that will be sent when we release the key.
The Auto Accompaniment works in a little different way, as there is a arranger software sending automatically several messages of Note ON and Note OFF, as there are lot of voices and notes playing. So if we change the regist while pressing keys of Auto Accompaniment (that is playing) meanwhile this part is sending automatically several Notes OFF messages of precedente style and the next Notes ON of next style meanwhile regist has called.
So only Auto Accompaniment can be working while change regist during one fraction time of a second. Or we can play Left, R1 or R2 notes whose are not continuous. So, e.g. we can change regist while playing arpeggios.
I hoppe this is of any help.