Challenge accepted :)
Shoot me an email or drop me a link on Twitter/G+ with a copy of the .Master that's causing you headaches.
Regarding IIS 6 setup it can be troublesome,
There's a tweak floating around the forum (which you've probably seen & tried)
which seem to relieve some IIS6 pain, One issue I've ran into that caused me sleepless nights was a little checkbox marked 'Verify that file exists' which naturally shouldn't be checked because we're talking about virtual files. But without knowing anything more it's a shot in the dark.
If you're just looking for a pain killer, you can also simply use <script> tags to load the other js libraries.