Hi Alexander,
I see you got punrewrite installed finally ... ;^) ...
Some suggestions...
1) You could try downloading the "Internet Explorer Developer Toolbar" to help you inspect things a bit.
2) Install Live HTTP Headers for Firefox and inspect the live headers. In order to best understand what it may should be doing you would do well to have a virgin PunBB installation into a separate directory where you can view 'normal' live headers behavior, and then make comparisons.
See if you can disable punrewrite for comparative testing. If you have a backup of the pages from before you updated your package, you could install that to a separate directory ... I wouldn't worry about the database (at this juncture). If you cannot do this, ask the person who implemented punrewrite for you (assuming it wasn't you).
Just some thoughts. Good luck.
TwoHawks
Love is the Function
No Form is the Tool