Let me try to describe my actions as detailed as possible.
1. Spawned on the John C. Stennis, hot start, attached to catapult 1 in the Aggressor skin with a clean loadout.
2. Launched, took a little low level flight. Landed at Tonb Kochak.
3. Parked. Without shutting anything else down first, I turned off my engines and straight after that my battery.
4. Rearmed with 2x Sidewinders on the wingtips, 2x2 Mk82 on the outer pylons and 2x2 19 rockets. 75% fuel.
5. Started APU, crank+start right engine. After succesfull start, crank+start left engine.
6. Press Stop on the BIT page.
7. Put flaps in Half for FCS Bit test.
8. Started FCS Bit test.
This is where the problem started. The FCS Bit test did not start. It only did the first test of the LEF and got stuck in there. (See screenshot)
After that, flaps and (takeoff) trim no longer worked. My flaps were stuck in this position, and I was unable to set takeoff trim. Tried the FCS reset button, it gave me a RSTRT on the FCS Bit page. Started again, same result. It was just stuck in there. Have some more screenshots of the issue if needed. DCS Log attached. I was unable to upload the track file to the site directly so here is a MEGA link to it. https://mega.nz/#!N1kg3ADQ!c8bivOs627RFySRhBRGHg-7Kpv0k9NprzuchVdAwe40
Hope I was able to help.