Basically, SH3 Commander is not being allowed to write to your game files. This generally happens because:
1. You are not logged in under the Computer administrator account. You must have administrator privileges to run SH3 Commander.
2. You have a firewall, antivirus, spyware or other system file monitoring application which is interpreting SH3 Commander's attempts to write to your SH3 files as malicious and hence blocking them. Try turning them all off and testing SH3 Commander again. If it works, turn the applications back on one-by-one, testing SH3 Commander in between. When it fails again, you've found the conflicting application.
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