All the problems with the installer will be solved with the new version (should be up in aprox 1-2 days).
If you manually installed, and get files different from server, you did something wrong installing.
Restore your backups and try again.
Heads up for 64-bit bugs, Game Directory not found for player models, but remove blood, explosive textures, and remove foliage work. Don't know whats wrong with the player models not being installed correctly. Followed all instructions, even did a file integrity check and tried to re-do the process. Still to no avail it doesn't work.
Edit: Also back ups do not work. The back ups go right into the same folder as the modified IWD's and not into the designated Backup Folder. On top of that it does not create the proper back up for 00, 01, 04, 06 and 14 IWD files.