I installed Titanium about 3 months ago and I had some of the same problems. In my case Titanium didn't overwrite the GFX or the AI folders, it just installed them as subfolders within the target folders. There was also another folder that wasn't completely overwritten but I've forgotten which one it was, sorry. I had to manually overwrite all three of those folders, but once I did that I got SXRC as the checksum and the game has played fine ever since.
I did originally try to fix it by moving the folders that needed to be overwritten into a Backup folder, and then moving the WiF folders back to the game directory, but that resulted in a CTD while loading.
Maybe someone will come up with a better, faster way to fix this problem but in a pinch overwriting manually will work, it just may take awhile if you have an older PC and/or don't have a lot of unused space on your HDD. It's worth the extra effort though, this mod is awesome.