permalinks still have index.php, with mod rewrite

Hello

I’m having a lot of trouble with a network install – I currently have three sites on one install, with domain mapping such that one of them is off at dev-m.org (obviously not a real url, but none of the sites are actually at real URLs), the main site is at dev-s.com, and the third is at dev-s.com/portfolio. That last is empty so it’s not a concern right now.

I’m trying to get permalinks to work, and I’m nearly there, but it’s not working. I can get to the pages if I use the “index.php/permalink” method, or default permalinks (?p=1), but not just “permalink”. I’m on apache, and I know for a fact that mod_rewrite is enabled – I have other WP installs that still work, and this one worked before I domain-mapped it (which also had me messing with virtual hosts, which is a bit out of my depth).

The issue I was having before was that I’d set up the virtual host wrong, so it could be that again… That file is here [at pastebin].

Alternately it seems that WP is just ignoring my .htaccess file – telling me it’s updated when it hasn’t (I had tested this by deleting the file, updating permalinks- and getting the success messages, but the file still didn’t exist when I looked). So if it’s any help, here’s my .htaccess [again, pastebin].

Hopefully someone can help me, or at least point me in the right direction.

Edit: I forgot to say that the ‘not working’ behavior I get is that it just displays the index page.