If you can reproduce this state, can you do a "kill -11 pidof steam" This will cause steam to send us a crashdump and if you send us the crashID we can see what the steam process is doing. Sounds like it was wedged somewhere.
Nothing extracted yet.
EDIT: This seems to apply to other games as well, but only games that use Steam achievements.
EDIT2: A steam restart fixed my problem. Still, this can not be intended behaviour!?
Here is the result for dungeons of dredmor.
Launching from the steam client does launch the binary, however the game never opens. Using "ps ax" I can see that the process is still running.
Launching manually from the game's directory does still work, but then it is not possible to unlock any achievements.
Here is the backtrace after attaching gdb to the running process: