I’ve found that when you start debugger from Flex using IE, in most of the cases the debugging session is stuck at the stage when Flash Player shows Loading/Initialising progress bar.
I can’t recall this happening in the Firefox. I still have got intermittent problem with debugging in both browsers but at the later stages, when I load and initialise dynamically SWFs and loading/screen update is stuck.
To overcome this I used to a trick: right-click to get into the Flash Player menu -> click “Play” to shove the debugging session. Sometimes it worked, sometimes it was crashing in the guts of the SystemManager. So I had to restart the whole thing all over again.
It is appeared that the culprit for this freezing is an Anti-Phishing filter.
As soon as added my sites to the Trusted domain and in the IE settings disabled the anti-phishing filter it immediately stopped doing this nasty thing.