I guess the problem is that you haven't done a clean uninstall. This is how to do it.
1. Remove EVERY trace of SH3 (that means run the uninstaller and delete all the files in the C\Program Files\Ubisoft\SH3 AND the SH3 folder in My Documents)
2. Install SH3
3. Patch it up to 1.4 using the appropriate version. That means you have to use either the European or the American version and the one for the CD\DVD or the one for Downloads (check the ubisoft forum for that) If you don't patch it up GW will not run properly.
4. Now you can install GW (you can use either the mod enabler or install it on top of SH3-If you use the mod enabler you can remove GW without having to remove SH3)
If you have any other questions fire away
Good Luck