Thanks for all the replies! I followed everyones advice -- no seriously, I used Attila's run() function, daperl's gtk.gdk.threads_init() code, and daniel's threading and mainloop tips -- and now it actually works.

The only problem now, is I'm getting the strangest xlib crashes occasionally, I think my threading is "not quite right". I'll look into it.

A round of Thanks in me!

Edit: I (think) I fixed the crashing by wrapping all gtk calls in my clipboard class with gtk.gdk.threads_enter() and *_leave().