Not sure if anyone has came across this issue. I'm using mostly B9 Aerospace parts for my space plane. When I attach mechjeb my controls appear to be switched around. For example, S/W for pitch is now yaw, A/D keys are pitch, Q/E appear to be working fine. I'm also using a pair of VTOL engines from B9. When toggling "VTOL" the left side ends up being reversed(engine exhaust pointing up). Once I remove mechjeb and back to launch, things are normal. I first noticed this when I updated KSP and my mods to the latest version. So I decided to rebuild my craft from scratch thinking something happen during the update. Not so. Running MechJeb 2.0.9, KSP 21.1 Ok. I did some more testing. The control surfaces were moving correctly on a stock KSP craft along with a stock B9 craft. It's only happening on the craft I made.