To all having the engine sound issue, I have figured out a quick fix, you need to empty the IDSkillfulR1 folder into the Squad folder inside GameData. I don't know why it fixes the problem, but it does.
I am having the same engine sound issue, I have tried re-installing skillful on stock KSP, re-installing KSP, still encountered the issue. Also, any chance of a "rods from god" being added?