Sean Wallbridge
Ran into this tonight and solved it in the only way I could sort out how.
Issue:
I imported/created a new master page that worked fine on all sites that inherited permissions from the top site collection (publishing collaboration portal).
However, subsites with unique permissions would not display the master page properly (however, it would display the existing master pages included in SharePoint). It was screwy, warped, messed up, whatever – it looked damn ugly.
Resolution:
Anyways, after some frustration and realizing the time (going to go have some beers with friends, much more important), I finally stumbled across this article (https://support.microsoft.com/kb/936908). While it didn’t actually help, it did make me think about the problem differently. I had different permissions for this subsite (using it as a pseudo extranet setup) and thus figured it was going to look different anyways. So, I just imported the master pages again (yes, chain broken but problem solved) into this site collection (thus they end up in _catalogsmasterpage) and then set the one I wanted at that point, to be the default master page.
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