I've been having the same problem with minimized programs disapearing? It started after I upgraded to SuSE9.3. At some point I rebooted and the panel was all screwie. I've just tried to add an External Taskbar. This accepts newly minimized programs. Yet, it's an added panel on top on the default panel. Going through the configuration, I've selected Show Only Minimized Windows in the Panel config for the Taskbar. Nothing?
If anyone figures this out, please pass it on to us.