PetJournalEnhanced is indeed a must-have add-on for pet collectors. It looks a lot like the basic Pet Journal that Blizzard gives you, but has added a bunch of options that make it so much more useful.
It does have the same problem that the basic one does. Guild Heralds, Guild Pages, Argent Gruntlings and Argent Squires only show when you are logged onto a toon that earned them. Unlike all the other pets, you won't see it as collected if another of your toons acquired it but you didn't. Plus a Horde character with, for example, a Guild Herald won't see an Alliance Guild Herald even though you have an Ally toon that has one too. Not a really big deal, it's not like you're going to do much with these pets that can't battle anyway, but does affect the total number of uniques it shows.
Solution, as other posts have pointed out, use the excellent Manage My Pet Collection feature this website gives you. It'll show you everything.