I have some information after getting this bug. I started a new save and worked my way through contracts, I used the VAB 6 times, building a total of 6 crafts. On the 7th mission ( the problem one ), I launched the ship then reverted, swapped out the the pilot then relaunched. I achieved orbit, did my deorbit burn and had no drag. The bug persisted through 2 re-attemps ( revert to VAB, launch, orbit, no drag ). I have not had a chance to see if it is effecting the save or not ( I doubt it but I will update you the next time I can play ). None of the other launches I did before the bug had issues, but none of those launches were reverted, all were landed and then recovered.