I had that happen on occasion on my Slackware system, and maybe a similar thing is happening to you:
Have a look in whatever you use to configure your "Desktop Settings & Appearance" type area. Investigate the way the taskbar and/or windows are displayed, particularly if you have multiple desktops or screens configured. Make sure you have checked such things as "Show minimized Windows on Taskbar" and "Show windows from other desktops" and stuff like that.
Any luck?
