The problem reported by Red Spade on thrust vectoring is not random. If I lower nozzles fully then they retract correctly otherwise they will retract fully. They must then return fully or they will go full down. Once you latch on you can work with it. This may be related: my flaps twitch but remain retracted although the HUD shows movement, this applies to AV8 and F18.
This is the CUP-JTW download.
Between AV-8B+'s thrust vectoring and all pack contents' flaps , they are no common problem, completely separated.
What game HUD says about your flap problem?
When you've installed all the requirements correctly, the positions of the flaps are in these 3 types:
AUTO / HALF / FULL.
As written in S3's instruction PDF, each aircrafts have Fly-By-Wire flaps and deploying degrees are decided by flight computer second by second. In example, in high speed, the flaps are completely retracted instead of switch position, enough lift force and no need to use flaps.... in slow speed and high AoA , the flaps are a bit deployed even the mode is AUTO.