This is a fairly new experience for me, I re-use old alarms so I only have about 6 or 7 in there. I can reproduce the problem at will: An alarm goes off, I press "Stop". The Stop button stays lit and the phone is completely unresponsive. If I wait for the screen to go off after the powersave timeout (1 minute in my case) and then unlock the phone, it unlocks and the alarm has cleared, but the hildon-desktop is frozen, i.e. none of the shortcuts or widgets respond. I can access programs via the task switcher, I can access the control panel, just hildon-desktop has froze, and this does NOT come back forcing me to reboot the phone.
This has been happening for the last few weeks, just before I installed hildon-portrait so it's not that at fault. I've used HWSync=1 for months without issue (and CSSU and PowerKernel47). Really can't think what has changed...