Is this with all distorted profiles or only with specific ones?
I'd suggest to see if this happens with the high-gain factory profiles as well. If that is not the case, it's the profile you are using. Concerning the output clipping: Check amplifier volume (3rd page of the amp settings), Cab volume, Rig volume (the volume next to the EQ dials) and all of your effects (e.g. EQs, boosters, etc. Everything that has its own volume parameter).
In case that does not help either, try recording a DI track and a wet track using a high gain factory profile, and post it here. This way we can double check the sound on our units to exclude any hardware problems.