@sarbian with the modset I linked you before, the shown ascent indicator is 180d off and in addition it looks like launch-to-inclination is also troubled.
(We spoke about this but I never made a ticket)

#739
See my imgur album of launch into plane of target in a very nearly stock KSP with just mechjeb and hyperedit installed.

I have been able to repro it by setting orbit altitude "too high" and fix by lowering orbit altitude. I believe I can therefore close this issue.