I found my issue last night. I had done Taming Eastern Kingdoms on my Ally but due to shared achievements and such when I swapped to my horde I'd see that Taming Kalimdor was done. I had thought I had done them all but I went around battling them all and actually found a couple I hadn't done.
Because you only need one or the other for Taming the World when you swap over it looks like you've done all the other ones.
It's a pain but I recommend just flying around and battling all the tamers again. Good way to level some pets and ensure you've got them all.
I printed a screenie of the list for each and just crossed them out as I did them...old school I know but better to be sure than miss one again.