I'm running the map editor tool from http://trac.wildfiregames.com/wiki/LatestRelease ("./pyrogenesis_dbg -editor") (sorry, not a very minimal test case). It does roughly the following:

Thread 1: call XInitThreads(); create thread 2.
Thread 2: create wxWidgets (Gtk+) window; create GL context (glXCreateNewContext); pass GL context to thread 1; run wxWidgets event loop.
Thread 1: adopt GL context (glXMakeContextCurrent using the display/window/context from thread 2); run rendering loop.

Thread 1 very quickly hangs inside xcb_wait_for_reply during various GL/GLX calls (xcb_glx_gen_textures_reply, Mesa's __indirect_glGetError, etc). Interacting with thread 2 (e.g. waving the mouse over the window) temporarily unblocks thread 1 and it usually continues correctly for a fraction of a second.

If I run with the normal Intel GL drivers, it typically carries on like this for seconds or minutes, and then hangs permanently.

If I run with LIBGL_ALWAYS_INDIRECT=1 then I get an assertion failure in thread 2 before the first frame is rendered:

  pyrogenesis_dbg: xcb_out.c:272: xcb_take_socket: Assertion `c->out.request == c->out.request_written' failed.

  (gdb) print c->out.request
  $1 = 5459
  (gdb) print c->out.request_written
  $2 = 5456

Currently running on Gentoo with libxcb 1.7, libX11 1.3.5, mesa 7.8.2. This used to work fine for me (from some years ago until some months ago - unfortunately I didn't track what libraries I'd updated when it broke). I don't know whether anyone else has experienced this problem.

I'm happy to provide more information needed to help debug this, but I'm not sure where the problem is or what's needed.