Some of them are. Your T5 is a Tremec, as are the T45 and 3650- all of which are stock Ford and none of which are considered to be spectacular. Does it only do it when it's cold? None of the linkage or internals are going to work as well as they can and should if it hasn't all warmed up yet. Do you have a good shifter on it? If you're still using the stock one and you shift hard, you haven't been protecting the transmission and it could be the synchros starting to go. If you put a good shifter on it quick, you may nip it in the bud.