OK,
hopefully I'm going to have a solution in the next release... lots of crossing of fingers here.
I've suspected for a long time that DirectX was doing a lot of multithreaded stuff behind the scenes, despite being told at startup time
NOT to; and given that a Direct3D 10 card is a multithreaded GPU, I also suspect that something weird, wonderful and undocumented (or obscurely documented) is happening here, even with Direct3D 9.
The next release should resolve all of that. Unfortunately I've short arms and deep pockets when it comes to graphics cards, so I can't personally test it.
I have however created an "Emergency Refresh 2" package, which contains the relevant updates. Grateful if those who have been having issues could check it out:
http://sourceforge.net/projects/direct3dquake/