There's a bug in Windows XP where sometimes the system tray tooltips and popup notifications will show up behind the taskbar, or behind other windows. This is really annoying when you want to use a tooltip.
There's not a known perfect solution to the problem. The way to make everything start working again is to do the following:
- Right click the taskbar, choose properties, and uncheck the checkbox that says "Keep task bar on top of other windows".
- Click Apply
- Check the checkbox again.
- Click Apply again.
This will temporarily make the system work right again, but you will have to repeat these steps if it happens in the future.
Update: Neosmart has created a small application that will fix this problem. The only thing is that the application will need to be running all the time, but if you have this problem often enough, you won't care.