I too have noted that there seems to be issues between SH3/SH3 Commander and the last Win-7 update in that on occasion SH3 will not load from SH3 Commander or fully shut down after a session.
Once everything is up and running SH3 and Commander appear to work as intended, at least on my system.
Recommend after a session, open the Windows Task Manager, click on the Process tab and scroll down to the "S" processes. If there is an entry for SH3.exe there should also be one for SH3Cdr.exe. Select SH3.exe and then End Process and both will close. This should get rid of the "...instance of Silent Hunter..." error message and allow you to run SH3 again.
No idea what Win-7 upgrade might be causing this but the KB90830 Malicious Software Removal Tool update from earlier in May may be a contributor.
-C
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