Or should I say, has anyone found a backlink checker that uses the new yahoo site explorer API? I noticed that most backlink checkers havent switched their programs over yet to use the new API info to pull the numbers...

All the commands that you use in the search like "site:" "link:" etc.. are now being redirected to use the Site Explorer... and Site explorer i believe uses a new API .. regardless when you try and query yahoo for the linkbacks, it throws a redirect, that redirect is messing up Yahoo link checker tools, because the people need to change the URL it is getting the information... which not many have done yet.
update your tools ppl!!