This has started happening to me too. Parallels won't hide when I tell it to, but will spontaneously hide at random and not show again. It started recently, so I'm wondering if its something to do with the Leopard 10.5.2 update...
On my system it appears to be related to an earlier attempt to Hide Parallels. Most of the time when I hit Cmd-H to hide Parallels, it works as expected. Occasionally though, Parallels remains visible. Then, at some point in the future, and usually while switching between apps, the Parallels window will simply disappear. The only way to get it back is to Quit from the Dock and reopen.
This problem seems most likely to occur when my system is very taxed for resources.
I'm on Mac OS X 10.4.11, Parallels Desktop 2.5 (Build 3214).
Just started today. Only change recently is that I've begun using coherence mode. I've been running parallels for 1.5 years now and never experienced this until now.
I experience the exact same problem. If I minimize the parallels window, it properly reduces to the dock, but then I can't restore it to a window. :-( The only solution at that point is to force-quit Parallels using command-option-escape. Any assistance would be appreciated.