@Fanuboat,
I suggest you print out your JSGME install and publish it here so we have a clear view of what you did install. (chose 'tasks' in JSGME).
Then, only YOU can know how you have installed SH3 initially. In the Progam Files directory? That's bad...Did you start with v.1.4? Are the files in your directory protected? They should NOT be protected. Have you applied the 4GB patch? Have you followed ALL and ALL instructions? It can be a pain to check all this, but only YOU know that. It's easy to miss something.
Also I would not use SH3 Commander before everything is ok without it (just to say; I don't know if you do).
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