I'm not sure about the bumps you're describing (are they a higher level than the sound that was just happening, or more like two dips surrounding a region at the previous level?) but here's what I've noticed so far.
The gap filling method fades to a 100 ms delay signal and then back to the real output signal. This is done just before the output, "inside" the output block or however you want to think about it. If what you're noticing is more like 2 dips, it might just be that the signals are out of phase during the crossfades. On preset changes the delay sounds for about 70 ms, on all scene changes or channel switching of any engaged block (whether or not it's in the signal path you're hearing or even connected to anything) it's about 30 ms.
This means that every scene change (or channel change of an engaged block) now creates glitches/blips in any effect trails or signal in the grid that wouldn't have been affected before--looper playback, synth, anything from an extra input, your own guitar sound (when nothing changes in the signal path you're actually hearing, which would have been glitch-free previously). USB audio from a computer isn't affected, unless it's going through the grid from an input block. The delay thing also happens during multiplexer channel switching to select amp blocks, but I guess a modifier on Mplex input source or amp bypass state wouldn't cause it.
I think this will create more problems than it solves for a lot of players who have already worked around gaps by switching between 2 amp blocks or finding musically suitable moments for channel switching. As it is now I'd rather not have any of the gap filling within one preset, but the preset switching seems nice. You just can't expect to play anything faster than about 8th notes at 100 bpm leading up to a preset change without hearing some kind of weird double attack on the last note.
Also: Changing any engaged block's channel in Axe-Edit or from the front panel will trigger the gap fill delay playback but not mute the live signal, so that can actually create a bump as high as +6 dB. And scene changes from the front panel trigger the gap filler but a switch (at Axe pedal 2 port) assigned to scene increment isn't doing it here. I haven't checked what happens with MIDI scene increment or direct scene selection yet, and no FCx here.
I hope this can be made optional, ideally with a setting for just preset change gap filling but nothing while staying on one preset.
