So I was recently attempting to replay the Port to test out the new APNG CB animations, but I got stalled on "A Small and Deadly Space", because the Orff wasn't arriving to allow mission end conditions. I assumed that I'd broke something with my many different mod directories. Then I was replaying my own "FS-Augmented" but I couldn't get past the first mission, because certain wings weren't arriving. After loading it up in FRED I noticed that the arrival cue of that wing corresponded to the destruction of a specific ship from another wing. I'd also noticed that another wing that usually arrives before you've finished destroying the first wing, wasn't arriving for some time afterwards. The arrival conditions for that wing was either a certain amount of time, or a certain time after either the first or second ship in the first wing. It then put me in mind of the Orff bug, for which the arrival cue was based on the destruction of a specific ship from a wing.
I maintain a number of older builds on my drive, so I stated going through them to see how far back the bug occurred. It seems that any build newer than June 10th is affected by this. It seems that if a specific ship from a wing is referenced in an arrival cue (and possibly other situations), than that condition will always come back false. There may be more to this bug, but that's the symptom I've noticed.