I've got windows 7 and i was having the same problem a while back, there was a multi step process that had to be followed to make it work correctly... i never found the time to do it.
now i have recently moved and my SH3 disk is put away in a box, rather than spend the hours finding it... i downloaded it on steam for $9.99
the process for installing gwx was a little trying but it was only a matter of figuring out where steam installs SH3
(C: - steam - steamapps - common - silent hunterIII i think)
anyhow the steam version downloaded and fired up no problem on win 7
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