Do not install the game, or Silent Hunter 3 Commander, in the default location in Program Files. SH3 Commander is probably trying to save some files in there and Windows won't let it. It's a UAC thing. Which can be avoided by installing the game and SH3 Commander into a custom created folder on your harddisk: like C:\games\SilentHunter3 and C:\Games\SH3Commander.
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