Well, I still don't know what happened, but I fixed it by switching to Foxit Reader.

I can print through adobe on the command line, and I made a quick utility to see the arguments being passed in and that worked, so the Print Server was running the executable, but together they did not work.

Foxit isn't listed as supported in 2016.2, although it is in 2017.1, but Foxit uses the same command line arguments for printing that Adobe does so I just pointed it at that and everything works great!