While I was running Rainlendar on my XP computer, I never had any problems with it hiding. I recently got a laptop with Vista, and I noticed that when I hit Win+D, or Show Desktop Rainlendar minimized as well.
The FAQ section for this problem
wasn't that helpful for me, as it still minimized even if the position was set as "On Desktop".
However, under the advanced options, changing Transparency type to Copy (or Region) as opposed to Native has fixed this problem, and Rainlendar now stays on the desktop (as long as position is set to "On Desktop").
For anyone that has been having this problem, it's worth a shot to try out.