Thanks for reporting this, we'll look into it.
Quick question: Is the armory updating each time you add (or remove) a pet? The Blizzard armory is known to be a little finicky at times, and if your collection data in the armory isn't updating properly, imports won't show any changes on WarcraftPets.
Testing if the armory is updating properly:
1. Cage a pet from your collection. Or you can add a new pet into your armory.
2. Log out completely.
3. Check your armory page and look through your Pets & Mounts section.
If it's there (or isn't there in the case of adding a new pet), then there's an issue on Blizzard's end.
A temporary work around: Use a different character on another realm (if you have one) to import from. The toon must be level 10 or higher and you must have recently logged on. That should allow you to update your WarcraftPets collection.