A couple of trouble-shoot ideas for comparison sake...thinking out loud...(I hope these don't aggravate you further as they may be obvious and you've already done this - I know - it sux when this stuff happens) :
- start with nothing else plugged into the axeFx but your guitar---cable---output---cable---amp. You need to make sure that the intermittent problem is not the fault of something in front of or after the AxeFx.
- Change your guitar, cables, and monitoring source
- if you have one, try a back-up MIDI pedal or other source from which you can transmit patch changes (computer, keyboard, etc.). Try to isolate that the problem is in fact only caused by your expression pedal.
- ditto with a backup expression pedal
- try using the AxeFx's dedicated pedal input for your Exp Pedal source (if you are currently using Exp Pedal via MFC), bypassing use of the MFC altogether.
In reading the OP, personally I'd want to be dead sure that the MIDI/Exp pedal wasn't the culprit here, and then move on to the AxeFx itself. I personally remember chasing down similar random bypasses and volume changes at the early stages of programming my Ultra, and eventually wound up cleaning out all of my pedal presets one-by-one to make sure only essential MIDI data was coming out of the thing. Seems to have worked in my case.
This may be getting a little deep, but if you have some kind of computer software MIDI stream monitor (MIDI OX), you could try connecting that to your MIDI pedal, and if you understand what all the hex means, you could see if something is corrupt in the stream, or if in fact your pedal movement is/isn't sending out a weird control value or other random nonsense.
Also, perhaps you could use AxeEdit and post up the .syx file of the offending preset(s). Who knows? - there may be a rogue controller set up somewhere doing strange things (doubtful, but you never know).
Another key would be to figure out whether this problem happens only with certain blocks within certain presets, or if it happens across all presets. Try bypassing blocks one-by-one to try to isolate the problem. This is time-consuming, but try rebuilding from scratch the offending preset, first with NO control/modifier features, and then taking care to make sure that only necessary control features are present. Sometimes in the course of deep programming it can be easy to lose track of Modifiers and their settings...been there before.
Worst case is that this is a purely intermittent problem. You'll have a longer haul ahead of you then as you slowly, one by one remove/add components to try to replicate the problem. 1st step is to make the problem go away! If nothing makes the problem stop and the only constant is the unit itself, then = service call.
