@andybot said:
The thing with the orient faces - if there are interior faces, it doesn't know which way to go, and often it will reverse faces you don't expect to have reversed. There is a plugin "remove inner faces" that may help make your model more of a "solid" and orient faces will behave more as expected. See if that helps your model at all.
http://sketchucation.com/forums/viewtopic.php?t=12668
The remove inner faces plugin didn't seem to do anything, too bad, sounded promising.