Well, it's the same problem that has been reported many, many times. Even again, it is reported just a few posts down from this one, with no responses, I might add.
While working in any window on the desktop, if the active window overlays the the Alarm window on the desktop, the Alarm windows will, in a seemingly random fashion, paint over the active window. The Alarm window paints at the same coordinates in the active window that it normally displays on the Desktop. Yes, I have the current stable build (129). Yes, I have reset all settings to defaults. Yes, I have cleared the check box, "Alarm window stays on top" in Advanced options. I am running the 32 bit version of Rainlendar2 on Windows 7 Home Premium SP1 with all current updates.
One of the posts describing the problem reported, the Alarm repaints when the countdown clock to the alarmed event reaches one minute before each hour before the event start time.
I assume that, since users have been complaining about the problem for so long and, since it has never been addressed, this behavior is considered to be a "feature". If so, it seems the time to, so rudely, interrupt the user would not be one minute before each and every hour but, perhaps, only one minute before the start time. Better yet, give the user the option of disabling these hourly reminders.