Two more things of note:
EJ of EJ_SA on Twitch noticed that the drag on the part behind the fairings is also getting a far too much drag as well. In many cases a fuel tank has two times the co-efficient drag of a flying brick.
Not sure if this is gonna cause trouble but :
https://www.twitch.tv/videos/245164428
He finds is about 4:16:00 in that video.
Secondly if the faring is loaded from a save and then launched (I'm assuming a sub assembly, merged etc). The problem with drag occurs. However if you completely remove the faring and add in a new one building it just like the one loaded from the save. The drag on the part drops to zero and never changes during launch. The part below it however gets crazy drag as before.
Hope this helps...
