Windows 98 S/E Due to HDD failure I replaced the HDD. Everything runs great except whenever I left click on my desktop (any location) the start menu items appear as if I had selected the start menu from the task bar.
On first boot after installation of HDD the ps/2 mouse and keyboard were pluged into the wrong ports. However the system was powered off before the plugs were switched to the right location. Could this have caused this problem? Or is there a setting somewhere?

Thanks
TripleJ

It it's also happening when you click on a Desktop icon, then you may want to consider reformatting the HD and reinstalling Windows.

Some Video cards have an option built into them that will allow that to happen
One your task bar you should see the Icon for your video cards program options.
Or you may have to use the display icon in control panel

Check what settings and options you have enabled.
Find the one for a floating start menu(As it is called in my video desktop)
and disable it. Depending on what video card you have the option name may / will be different