Also, you haven't turned off just 3d acceleration, but ALL acceleration from what I understand. To turn off 3d you'd have to disable DRI or turn off AIGLX so that the software rasteriser is used. Something like that anyway. I think your problem is possibly EXA related, but FYI if you wish you could probably be a bit more selective on the acceleration you turn off.
Also, you haven't turned off just 3d acceleration, but ALL acceleration from what I understand. To turn off 3d you'd have to disable DRI or turn off AIGLX so that the software rasteriser is used. Something like that anyway. I think your problem is possibly EXA related, but FYI if you wish you could probably be a bit more selective on the acceleration you turn off.