I just noticed this problem too. I have encoded Star Trek Voyager DVD (pal) and they don't have the HD tag. I had to reencode one episode in season 4 recently since I had thrown it away by mistake and noticed that it shows up as HD on the AppleTV.
I encoded the show with HB svn2239 and the missing episode is done with svn2596. I used the AppleTV preset + cabac and ref 4, b-frames 3.
The episodes are approx 752*576 pixels, but the one encoded later with rev 2596 is 776*592 which is probably why its recognized as HD. I don't know why it is encoded in a slightly higher resolution?