We have a different CMS, so I don't know if the search works the same, butwe use full text search through the AT Browser and Search Windows.
In our CMS, we have multiple item types defined, but only one of them has full text search enabled. So, to do a full text search, we have to select only the item type that has full text search enabled on it in the Search window.
Like I said, I don't know if this is similar for PDMLink or not. If it's something more complex than that, you may need to look at the database server that's doing the indexing to make sure everything is running properly. Good luck.