This used to be characteristic of some older viruses.
My guess now is that you may have dueling mouse drivers (eg, windows' driver conflicting with like say, a Logitec driver). Uninstall your OEM (eg, Logitec) mouse driver and try operating with only the Windows generic. (Note: If this is a problem there are ways of getting around it, but it involves some trial by adjusting things in configsys; eg, disabling the schizzel.)
Also, presumably you are using a USB mouse. Sometimes there can be an interrupt sharing issue, but usually the symptom is erratic mouse versus disappearance. There are ways to adjust/reassign IRQs, but you need to research this.
Finally, also check the BIOS. Sometimes there are settings/adjustments related to USB (and even cursor) control there.
Things like sound, video and even cursor control can have multiple overlay in windows. For example Windows has controls for sound, overlayed on any installed sound application (eg, Creative Sound Card Studio) as well as sound control for the specific player that might be used (eg, VLC Player). These can all operate in series or interact in unexpected ways. Ive found that sometimes just the order in which things were installed can make a difference in how the total system responds/behaves.