I strongly suspect that the answer to the riddle lies in the DP files.   Like the several different versions of the Alpha Weps packs that were/are available at various locations on the web, there are probably several different DPs for the same aircraft....particularly since there are  so many versions of the AlphaSim planes posted.   For example, these excerpts from your F4 DP.  My Alpha F4s don't look anything like this:

mount.0=wep_usmodern_f4pylon_out, 1, 1
mount.1=wep_usmodern_f4pylon_out, 1, 1
mount.4=wep_usmodern_f4pylon_inwinder, 1, 1
mount.5=wep_usmodern_f4pylon_inwinder, 1, 1

 

However, I would need to examine your particular version of the AlphaSim plane/planes to be able to analyze the possible issues with the DPs.  And I would need some screenshots of some of your CFS2 folders.  LOL. 

I've been involved with CFS2 since the sim came on the market, and I have forgotten more about it than I remember...plus I still learn something new about it from time to time.