Sometimes AICarriers.NET can take a little while to completely close down and clear the computer's memory of all it's "stuff".
Try ensuring sufficient time has elapsed after closing down FSX(A) for AIC to close. Maybe go get a cuppa joe, or a Ham-n-cheeze sammich. Also, you might try opening the Task Manager, Processes tab, and checking to ensure that AIC has closed completely, and correctly, PRIOR to restarting FSX(A). If not, close it out with the End Process feature of the Task Manager.
AICarriers.EXE, the older, JAVA based version, had a problem with not shutting down when FSX did. I, personally have had this little problem with the new, .NET version, but only very, very seldom. Not at all since I started modifying the FSX.cfg file with things like Kosta's changes, and so on. What I may have done to prevent this problem, if I in fact did anything at all, I haven't a clue, though.
A note as well: if you're using the EXE.XML file to start AICarriers.NET when FSX(A) starts, a little trick I use is that I made a shortcut to the AICarriers executable file, in the same folder as the AICarriers' executable for ease of finding it, and set it to always start the executable (AICarriers' .exe file, not to be confused with the older, JAVA based's AICarriers.exe) as Administrator, then pointed the EXE.XML file to the shortcut, as opposed to pointing it directly to the AIC's executable.
I us the phrasing "AICarriers' executable" to prevent confusion with the older, JAVA based AICARRIERS.EXE version. Every time I refer to AICarriers in any way, unless I am very specifically referring to the older version, I am referring to AICarriers.NET.
Finally, if you're using TackPac and CCP, there's a quicker, easier way, as far as I can tell, to start on a carrier's flight deck, or even the Hangar Deck. I have been focused on integrating HARM missiles onto the FSDT's F/A-18C, and dealing with a broken patella (kneecap), plus a broken wrist, so I haven't even loaded FSX@WAR or CCP, so I can't speak to how well this method works, if it works at all, how easy it is to use, etc. In any event, you might want to look through the TackPac forum, specifically this thread:
https://forums.vrsimulations.com/forums/phpBB3/viewtopic.php?f=108&t=19028#p124351
to see how to start up aboard a carrier. As I recall, there are several threads about this subject, but I may be mistaken.
Hope something in all this rambling is a little helpful...
Pat☺