Sorry for poor form. I'll edit if need be from now on.
I did get into a round with others, but they eventually left, with the last one left saying I was a bit too rough. I apologized and offered to team up with him against some other players on another server. He left. I hope that didn't offend him.

Now when I connect, 1.3 is used. I'm seeing "Protected lump authentication failed." I was seeing WAD and password errors before. Normally I would think this is just a game that doesn't like wine, but it ran fine in single player, LAN, and a few online rounds.
Edit: forgot doomseeker screenshot
edit: I think I found the problem. If I run doomseeker within my wrapper and join multiplayer from there instead of the launcher, I can get in. The only exception so far seems to be servers running zandronum 1.2, which I can still join if I set doomseeker to use the old zandronum.
So it looks like I need to fix my wrapper. Does anyone have the command line args for the launcher or zandronum? If I can get those, I can use the native doomseeker rather than bundle everything together. Specifically, I need to know if there is a way to tell it to look outside it's own folder for game files downloaded by doomseeker and how to pass the IP and port of the server to zandronum.