The C: drive is generally your OS drive, and as such contains the "hives" for the Windows registry that holds all of the information for you software installs. Did you re-install SH3 after the OS re-install so that it is in the registry and recognized as valid? You could re-install it to the Programs Files on the C: drive if desired, and run the modded or stock game from the F: drive. Use MultiSH3 for another Save folder. You would most likely also have to re-install the DirectX v9 files and codecs also.
