The base href should be the full url to the page that would appear if you didn't use a mod rewrite. It basically tells the page what the relative location of the page is when it can't get it from the url because of the mod rewrite so you can still use relative paths for images and css. The base href should include a page name.
Once it works properly with the actual page and the base href is pointing to the page, then the mod rewrite shouldn't break anything. I'd start by getting it all working without the mod rewrite or base href. Then add the base href and then add the mod rewrite. I don't feel like the issue is with the base href... it is just confusing matters.