Before I started having this problem, I use to have around 10-15 icons in my taskbar. Now when I start up windows I only have like 3. I know those tasks are still running because of taskmanager but they are no longer shown in the taskbar. anyone know why? And no window is not hiding inactive icons because I dont get the little arrow that show inactive incos.

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Did you set your Tastbar/system tray to ALWAYS HIDE some icons? If you didn't, you can at least check the Properties for the Taskbar and determine if somehow that is the case? Also, have you scanned your machine for any malware/virus' in case some play with what you have running. I've seen the recent Windows Update problem make desktop icons disappear when the SVCHOST.EXE had problems. You never know, make sure your machine is totally up to date on OS, application and virus patches.