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
Over at Subsims they have a few threads about this problem and similar ones.
Windows Vista: Installing SH3 and Patching 1.4b
1.4b patch wont load
You may want to post your question over at Subsims to if you still cannot get it working.
Let us know how things go and if you can get it going after trying the above suggestions.