I suppose that you have already tried to force the image subset alignment by select them in the list, and right click-align selected photos, haven't you? if not, just do it.
I've found it sometimes help if you select a small collection of photos around those reluctants prior to use align selected photos command.
AAAAAAA[AAAA]AAAAAAA
AAAAA[AAXXXXAA]AAAAAA
AAAAAAA[AAAA]AAAAAAA
If anything works, you could try to use manual tie points which are markers without coordinates that connect aligned photos to non aligned ones
Good luck