I have windows xp sp2 and when I try to quit skype it clears my desktop and loses the system tray
I have to do a reboot to get back.

Please check following:
Press control+alt+delete, do you have explorer.exe running?

If not then select from taskmanager to run explorer.exe.

We are working on that problem.

I've run into this problem too. explorer.exe is running when this happens.

Kill explorer.exe and start it again.

This is temporary workaround for this problem.

We are working on fixing it.

I had the same problem. It's very annoying.

It looks like the solution is to disable the Extras Manager auto start in the Skype Advanced options.

It worked for me. Hope it helps.

Thanks,
Paolo