Thank you nickrose to clarify the problem here!
I think it is very understandable. All the (rack-based) multieffects I have tried have this problem.
The reason why I see the problem as more serious on the stompboxes, is because you have the clean soundsignal going through the unit, not like with normal effect-setups through effect-sends from a mixer, in which case the clean signal isn't effected when changing algorithms on the unit.
If you are using the the Pitchfactor's diatonic effect, and then want to change to the H910/H949 effect, you first bypass the unit, then you have to step through 5 algorithms before you reach H910/H949. Each time you get a large audio-hickup!
At the moment I have switched to RELAY bypass-mode. In this case I in the above example get a small hickup, when I bypass the unit, and a larger hickup when I turn the next effect on.
This gives less hickups if you are switching effects alot.
That said I think the factors are fantastic machines!!!!
All the best