From what I have read this dll problem has happened to other people.
When you uninstalled SH3 did you run a registry cleaner after that? If not you should.
Uninstall SH3 again, run a registry cleaner, then install SH3 again.
Patch to 1.4b. Make sure you have the right version of patch1.4b.
Here is a link to these different patches -
Silent Hunter III Patches http://silenthunteriii.com/uk/updates.php
Over at Subsims they have a few threads about this problem and similar ones.