I recently upgraded to WP 2.3, from 1.5 and am having a problem with permalinks.
In 1.5 WordPress would write all it's rules to .htaccess, but now it saves those in a database.
At the beginning of my .htaccess I rewrite anything that begins with a page called galleries:
RewriteRule ^(galleries)/(.*)/?$ /index.php?pagename=$1&page=$2 [L]
so that I can handle these separately.
However, since upgradingto 2.5 this hasn't worked. Some of the links just end up redirecting to the top level. What I think is happening is that the rewrite_rules in the database are clobbering my first rewrite in .htaccess. If I turn off permalinks entirely (i.e. no rewrit_rules) then my above RewriteRule in .htaccess works fine, but if I turn on permalinks in WordPress is ceases working for most links.