I have trains deadlocking my rails because they 3-4 are waiting for a specific station to open up. But that station has a combinator wired to it with a condition using the Limit Trains signal, set to one. The station itself has the same thing, enabled train limit set to one. Any help? I would post pictures but I'm new here and don't know how- if its possible at all.

If you use LTN, you should not manage the train limits manually. LTN will ensure that not too many trains are sent to a stop (you can control this with a signal).

This is one of the areas where the code base shows its age. The "max trains" logic was implemented before there was a train limit per stop and uses its own calculations on how many trains to send to a stop. For a reimplementation, the code would probably use the train limit API.