Hmmm, BC is installed on my Win 7 PC in C:\Program Files (x86)\Activision\Bridge Commander. When I download a mod, I first extract all the folders to my desktop and then manually copy them over. Win 7 prompts me that it already detects a 'data' and 'scripts' folder and prompts me to merge the folders, which I say "yes". This is the typical method I use to install ships and have no problems with using them in the game.