'AlarmToday' has a setting to 'fix this' too. AT is sortof ppc2003 software, for example no VGA graphics yet though. This might mean any 'tweak-like' fixes it has probably won't work, but It is also running a parallel timekeeping system which stands a much better chance to detect any OS alarm bugs than you do.
Perhaps give it a shot, so far I can heartily reccommend it, since it has 2 key features (key for me, anyway):
1/ It has volume control independent of the system volume, so it can set volume to 'very loud' even if you have turned your system down to mute.
2/ It has full integration with the native alarm applications. If you want musical alarms then it uses alarmtoday's own system, but regular alarms will show up in your other apps too, and alarms made by regular apps will be 'enhanced' (i.e. the volume thing).
http://www.pocketmax.net/alarmToday.htm