I'm having the same problem with BAMT 1.2 as well as SMOS and NotSMOS.  For BAMT 1.2 I even tried applying the newest drivers and recompiling cgminer, didn't help.  Not sure where the problem lies, but you're not alone.

SMOS had it's own issues with freezing, and the Cards would appear and disappear from the status.pl web interface thing, just like in GPUMON.

It's happening to me to, with BAMT 1.2/NotSMOS.  I'm using two Gigabyte R9 290's.

Sometimes the web interface will drop to 0 and show neither card, and sometimes the browser will just refresh to programming jibberish with the error:
"Can't use an undefined value as a Hash" and then it complains about not being able to write to a death log file because of file permissions.  ANd 10 seconds later it will autorefresh and show one or both cards running.

LXTerminal is also flakey for me, usually it's the second card (GPU 1) whose entire column disappears, and then when it does reappear it's full of hash rates, like it was being recorded the entire time.