It sounds like there's a problem with your field mappings. If you run PetFinder manually from the publishing menu it should tell you. I suspect you've added a new breed or species under Settings->Lookup Data, but you haven't chosen a matching publisher breed. Look for ones with a blank value in the publisher column.
It doesn't look like there are any blank fields and I've run publishing manually a couple of times now. It looks like Adopt-A-Pet is up-to-date and talking to ASM properly. This seems to be a PetFinder issue.
Are you getting an error message when you run PetFinder? There should be an error message or a log file and it sounds like you aren't getting the latter. If you use sheltermanager.com you could email us at [email protected] with your account number and we'll take a look.