bkrumme
Experienced
You aren't mixing ownhammer IR's with stock or redwirez ones are you? I do remember reading on here that there was something with the way they made their IR's that would introduce a different amount of latency than other IR's...which would cause phase issues. Only if using 2 cabs @ once though, and I think Ownhammer was in the process of correcting that. Where are you panning the tracks in the stereo field, this may shed more light on your M/S mastering wierdness. From the sounds of it you are using seperate mid/side eq and multiband compression in mastering? In my experience while the Axe does emulate the things I like about tube amps when recording you cannot treat an axe IR track the same as a tube amp tracked with mics, they are just not the same.
This is a good point, though I haven't tried to mix Redwirez with Ownhammer or either one of those with stock cabs. I was under the impression they were all phase aligned with the stock cabinets, though.