I've had similar problems myself. For instance, if you use
boostor some similar process-control tool to kill the Skype.exe and SkypePM.exe programs, the processes disappear from memory but the system tray still shows the Skype icon until you move the mouse over the icon. Then the tray refreshes, the Skype icon disappears and the remaining icons rearrange.
On Experts Exchange I found a bit of Delphi code which moves the mouse over the systray (using system messages rather than moving the mouse pointer itself.) This convinces Windows to update the systray. Because not everyone has an Experts Exchange membership, I've turned the code into a COM DLL, which you can download. Source is included (Artistic2 license.) A copy of the original Experts Exchange code can be found here.
Once you've registered the DLL (regsvr32 UpdateSysTray.DLL) you can use it in anything that supports ActiveX/COM objects. For example, in VBScript:
© Copyright Bruce M. Axtens, 2008