Why does the alarm on my HTC Desire not work correctly?

I have setup three alarms on my HTC Desire (running standard 2.1 with Sense). 1. Mo, Tu, We, Fr @ 05:45 2. Th @ 05:30 3. Sa @ 07:00 They are set as repeating alarms and the phone displays the little clock symbol in the top right corner indicating that an alarm is active. I have been running the phone with DeskClock activated each night and this also says that there is an alarm active for 05:45 the next morning. However I have watched it (with it not working for some strange and bizarre reason I am waking up before the alarm goes off) and at the time the alarm is set for nothing happens. Can anyone shed some light on this? My wife has a HTC Hero that is also running 2.1 and her's appears to be working correctly. I also have ATK that is running and is set to auto-kill running applications and I have been wondering if this is the cause, however this does not kill the DeskClock app that is running so I am not sure if it is relevant.