Umm, I'm pretty sure the Protection Error is talking about the fubar StarForce protection system.
As yet there is NO compatibility fix for Starforce & Vista. This was admitted by the SF developers.
There is only one way to allow SH3 to run on a Vista system which has issues with SF but that is not allowed to be linked to here on Subsim.
Needless to say, you will have to find a way to run SH3 without the Disc in the tray.
I've said enough *poof*.......