User is running windows 98se.

On startup, the first thing I see is a gray window named desktop. In order to get to the right side of the box, I need to keep moving the window to the left for about 40 screen widths only to find there is no "x" to close the window. Double-clicking on the top left corner does not close it, and Alt+F4 does not help either. That particular window can be closed by pressing enter & the desktop loads, but the same thing happens alot of other times & won't close. For instance, if I attempt to format a floppy disk, the window appears with "format 3 1/2 Floppy" as the name. If I try to run edit.com, the window comes up with an "edit 'filename'". It appears to be completely random and have no consistencies with file extensions or types (not all .com extensions do it, not all executables do it, etc.). Any help would be greatly appreciated as reloading the system would be a pain in the A**.

The PC has all the windows updates, scanned for viruses, adware, spyware, etc. all are clean. Tried replacing video card... no good.