I've recently purchased a Modfactor with V3 I have noticed this happening too.
In bank mode, when switching between two banks, say #1 is a phaser and #2 is a flanger, when I press the footswitch to change effects, there is an audible gap (or hiccup as the previous poster said) of a couple of miliseconds, almost like the Modfactor is loading the next effect. This also happens when I turn off one effect, and then go to another effect later on.
Is this normal? It's kind of bugging me a little bit, as I don't really want to be playing on stage and going to change to a new effect and my sound hiccuping, however briefly it might happen.