Yeah thats what I thought. Is there a reason that you're using 2 methods? I'm just wondering why the flag method isn't being used for the covers. Also I've just had a quick look at it and noticed you're already using the resolution method for the flags if 'bluray', etc isn't found in the filename.
Anyway as a fix for now I've changed my viewtype_showcase.xml and viewtype_slimfiles.xml to
Code:
[stringcompare(ListItem.VideoResolution,720) | stringcompare(ListItem.VideoResolution,1080) | substring(ListItem.Filename,bluray)] + !Skin.HasSetting(HideVideoCase)
in the visible tags where the covers are setup and its working.
If you haven't already seen it theres a bit about the stub files here
http://wiki.xbmc.org/index.php?title=Media_Stub_Files and here
http://trac.xbmc.org/ticket/10384
If this is something that you add more support for in the future I think it would be really nice to be able to filter between online and offline content - maybe like you do for HD movies at the moment and maybe have an extra flag or some way of really separating and/or identifying stub files.
You probably hear this all the time but it is a great skin, your doing a great job with it.