Ok, I did search the aircraft.cfg file and they didn't come up with anything to do with "ChasePlane". I think that it would be highly unlikely that Steam reverts back the .cfg file, as I've installed skins with to the Aerosoft, its only if you ask Steam to "Verify integrity of game files..." http://prntscr.com/f13y5w
Whilst I was writing this, I decided to try and edit the .cfg file, and write "Please don't remove this line of string" and it couldn't save, then I noticed that I had FSX open, and decided to close FSX, and try and save it again, which it worked.
Well, I guess everything up there is what to do with trouble shooting. Just going to tell you, ChasePlane can't modify the .cfg files whilst FSX is running, so I ran ChasePlane without opening FSX, and it changed the .cfg files, and now it works! I guess the fix is run ChasePlane without opening FSX at all. Thanks for the help!