[Paul Riley]

As Jim said,it sounds like a lot of junk has accumulated in your registry base,cleaning this COULD alleviate the problem but is not guaranteed.Either clean the registry manually (a risky endeavour if you dont know what you are doing!) or buy a certified reg cleaner from say Amazon,or you may be able to find some freeware online.
The only safe way to return your system to its factory defaults (original working order) is to format the entire system.By that I mean insert your original operating system disc (if you have it) and clean install the entire OS from scratch again,making sure to back up all important files,like saved games etc.
This WILL guarantee the return of your original system and restore the default windows installation files needed to install stuff,and probably allow you to install SH3 again properly ONLY if you are sure there is nothing wrong with the SH3 disc and it has worked before with no problems.
If your system was built for you by a friend for example you may not have the original OS disc at hand,in which case it may be prudent to buy one.I still use Win XP home edition and its still a rock solid OS,although the Service Pack 2 has been known to cause problems with games and is quite bulky in size,a whopping 400MB I think it was!
Sorry if this is no help,but formatting WILL remove all problems that were not there before.I personally carry out a format usually once a month or so,just helps to keep her weight down by removing all the uneeded,and likely corrupt junk.