Did you delete the SH3 folder in (My) Documents? And the game's installation folder when you de-installed it? There might be some leftovers from your possibly corrupted old install. Re-installs have been known to fail sometimes because of this.
It might not be related to your problem, but since Vista the following is wise to do when games/applications will end up getting modded. When you do reinstall, I suggest you avoid to install it into the Program Files folder. Make your own folder like C:\Games\SilentHunter3, and put it there. Windows doesn't like it when files in there get modified and throws up UAC warnings. Or outright cancels/overrides it if your account isn't an administrator.
[Edit]Which mod-parts are enabled in the JSGME application? The GWX Late War Sensors mod-part might cause issues if your career doesn't match it's requirements. Or one of them would anyway.
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