Every since I got my 10.4.8 update to OS X, iCal alarms have been appearing mostly off the screen. It seems a lot of people are having this same problem and Apple is working on it (see Bug ID# 4759919).
Steven Frank accuratley dubbed the behavior "shyCal", with a screenshot of the alarm display problem, although mine is off to the right side. Weird.
I've tried blanking the plist. I've tried repositioning before closing (heck, ya have to!), but –so far– there are no quick fixes.
If anyone sees a resolution for this, please email me or hit me on chat. Thanks!