I have finally understood how it is possible to reproduce the problem and how you can temporarily force the alarm to stay on bottom. Here is how to reproduce the bug.
Of course, you must untick the advanced option "Keep alarm always on top".
Create an event (or task) so that it will trigger an alarm as soon as possible, and close the dialogue. Wait. When the alarm is displayed on screen, open any window (I use Explorer) and place it partly over the alarm so that you can still see the "overdue" message and the calendar. Wait. When the message will be refreshed to show that the task is overdue since one minute, the alarm window will jump on top of the Explorer window. Bug! You can click the Explorer title bar to bring it on top, but the next minute, the alarm will jump on top again.
Now, to force the alarm to stay on bottom, just left-click the calendar (not the alarm!). Nothing happens, but the alarm window will stay forever below the Explorer window.
Unfortunately, as soon as you open some dialogues (such as the manager window), or when a new alarm is triggered, the bug happens again. You can click the calendar again to solve it temporarily.
So, I'm now sure that that strange behaviour is caused by a bug. When some windows are activated (for example the alarm window itself, or the manager), the bug happens, as long as another window (the calendar) is not activated. I've tried to reproduce the "solution" explained above by clicking on the Todo or Event list windows, but that doesn't seem to work (although I'm not totally sure).
That means that the calendar window MUST be on the desktop, and that you have to click it when an alarm has been triggered, or you will have the alarm jumping on top every minute.
I've tried also the X32 version, but it has the same bug. I have used that version without modifying anything, except unticking the "on top" option and creating one simple event to test the problem. So, I'm now also sure that the bug doesn't depend of my configuration or skin changes.
Any chance to have that bug fixed in the next version?
(I forgot to write that I use Rainlendar in portable mode, if that makes a difference.)