I've never had to do a fresh install of FSX/Acceleration to get Captain Sim add-ons working.

Having FSX originally installed in C:\Program Files (x86) could explain the problems. I know that other developers of complex add-ons for FSX DO NOT recommend that FSX is installed in the default location on Vista/Windows 7 (and probably Windows 8 is added to the list now), due o the security those OS's have over that location.

Anyway. I'm glad you got them working now.