I'm not sure about details but as far as I remember Windows CE uses a brilliant approach to fix this bug. System tick count is set to value equal three minutes before overflow. And system counter overflows three minutes after OS starting. 3 minutes usually enough to load all applications that could be buggy but this time is less then usual debug session.

edit: found details:

http://msdn.microsoft.com/en-us/library/ms885645.aspx

For Debug configurations, 180 seconds is subtracted to check for overflow conditions in code that relies on GetTickCount. If this code started within 3 minutes of the device booting, it will experience an overflow condition if it runs for a certain amount of time.