Holy handgrenade, batman! This has been back in DO since early 2009?! Over time I've been banging my head against my desk 
several times, when I found the filters not working in flat view, but never did a proper search in the forums. I usually read the change log, but somehow I must've missed that one. 
Just started using Subversion, wanted to hide the ".svn" dirs and decided to give it a proper search this time.
In fact I hadn't even noticed the "Advanced" section in the Preferences. Awesome.
Thanks guys. Life on the computer would suck without DO.