I have been experiencing the same situation.
PHP 5.3.3
WP 3.0.1
As a server admin – the solution that I found to resolve the issues with a lot of scripting issues was to simple down grade my PHP version back to build 5.2.14 and this took care of the permalinks issue.
Hope this helps
Randy Howard
CEO
http://www.wmthosting.net
One problem that I see here – which file are you making the changes to?
There a lot of files in WP.
Thanks
