Have you tried caging them and then re-adding them to your Pet Journal? How about checking on an alt character (level 10+ and recently logged on, if you have one) to see if they appear in the armory collection?
This sounds like an issue with the armory, and as such you could always submit a ticket and see if Blizzard CS can assist.
Feel free to browse through Perks N Peeves
, my vanity pet collecting blog!