I use Xtart to start fluxbox, although using startx leaves me with similar problems. I did look at the processes but could not spot anything obvious - although,in fairness, I'm not entirely sure what I'm looking for!
I also looked in .xsession-errors, and again I can't see anythnig immediately obvious.
I tried KDE to see what happens and there is no problem, so this is clearly a flux problem.
Once I have lost X I can do nothing with any input device - so no keyboard combinations work at all.