Before you installed did you ensure all remnants of previous SH3 installs had been purged from the registry?
If I recall, what I did was DL from steam. Booted it up (not sure it this is necessary). Closed out of it. Ran the GWX3 install and then installed the SH3 Commander mod. After that I installed the GWX3 compatibility patch for Sh3 Commander.
SH3 Commander is not necessary, that was just the sequence I did my initial install.
I also run as administrator if that matters.
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