WordPress and Custom .htaccess
I’ve found that there is a problematic combination involved with a server-writeable .htaccess file, and a .htaccess file that you have modified. If you put in your own custom edits; for example a download redirection script, then click the Options -> Permalinks section of the weblog control panel, it will overwrite anything you have done to the .htaccess file “automagically” (even without clicking the “Update Permalink Structure” button).
This might be a feature, but has caused me many a headache. So, since I doubt I’ll be changing my permalink structure anytime soon, I made it unwriteable.

