As you suspect it is probably registry problems.
Download Reg Scrub XP, freeware and the best registry cleaner out there -
http://www.majorgeeks.com/download.php?det=2048
Try running that then attempting the install again, if that fails you may want to try to uninstall Baldur's Gate II completely (inc. SoA), empty your override folder in the BG2 directory, run Reg Scrub then install all over again.
Make sure your versions of BG2 are patched when running Reg Scrub again in the future, I'm sure there is a bug in unpatched SoA where registry cleaners delete a key and the game isn't recognized as installed (though I don't believe that to be your problem)