I was using my Powerhead through a 2x12 with V30s and I had the same issues. I did set the monitor out EQ to adjust the sound to suit the cab but some patches just sounded odd through the cab but great through a PA.
My fix was to try to stick to amps profiled with a similar cab to mine. Those offending artefacts seemed to fade then. The cure was going FRFR but that's another matter!