Using Assets 2.0.5 on EE2.5.5
When I remove index.php using Ellislab's official method Assets simply stops working. It's hard to explain without screenshots, but on existing entries all thumbs are gone and when you click add or remove file in an entry form you simply get a blank screen. More specifically what especially seems to trigger it, is leaving "Name of your site's index page" blank, the htaccess file doesn't seem to be the issue. More specific if I make Name of your site's index page blank, the behaviour happens, if I put index.php back it's working fine, even with the htaccess file.