I had a scope hooked up to the bus lines, and just saw activity. It turns out that since there was no 'awake' node, the CAN card never got an acknowledge from anything... because of this, it kept sending it's last message until it saw a responce from something.
I had ignored any errors that were just warnings, since I had other issues as well that was warning me (maybe I should have looked at those a little closer too 🙂
Anyway, now i've hooked up the two CAN channels and have the one just listening and giving the needed responses, with no data. Now when I start and stop CAN, it does what i'd expect.
Thanks for the help, though I had suspected this, and finally got a response from tech support that it's what the problem is.