The same thing happens to me, but it happened with the 3.50 update 4th or 5th preset I think, the Brit one. And some horrible over-distortion happened just when I bought it with the Panama one with 3.15 update I think it was. It was horrible.
For what I've read, it happens to some people when trying several presets in a row (which I was doing then and yesterday). Some say it's fixed with just restarting the unit (not reset needed). Others say reset...
I've seen some saying they can only get rid of it turning down gain and/or volume in the amp, so if they want more distortion they have to put a pedal before it, and I imagine not as a boost (as it would end up creating the same situation of too hot input) but as a distortion pedal or overdrive.
I used a Jaguar Kurt Cobain signature; I think it's humbuckers are quite hot (high output). I'll try with a Cort X1 in single and humbucker mode and an RG2228 with active EMGs (I'll use padding).
I'll try some things, if I find a solution I'll tell.