I've seen the programs in the taskbar get rearranged if "explorer.exe" (the program that runs all of the pretty Windows stuff) crashes or is killed abruptly. Does the whole taskbar go away for a moment, then come back with some programs missing and/or rearranged? If so, then explorer.exe is probably crashing. Beats me why, though.
I would recommend running a virus check, uninstalling any old software that you don't use any more, and defragmenting your machine. In other words, do a computer checkup and make sure it's running in tip-top shape.