When you take a mod out of SH4, it should leave your SH4.exe the way it was with the Compatibility settings. However, especially when changing out a major mod, such as FotRSU, you do have to empty the Save game folder again, else you have a combination of FotRSU and Stock (or whatever mod you may have added since). Navigate into C:\Users \UserName \Documents \SH4 and delete everything, then try to run SH4.exe again.
btw - you will have to re-set all of your Options for the game...