I am going to predict this an optical mouse, plugged into the USB port. I had a similar issue before under 2000 if I remember right, though it may have been XP. Anyway, after doing much research on google and usenet, the only solutions I could find was an IRQ conflict with ACPI and your USB/mouse. You can try to disable ACPI/Power Mgmt. both in your BIOS and your control panel and see if that resolves it. I ended up buying a new mouse, both because I was pissed at that happening frequently, and wireless mouses are neat-o.
Oh, and if my assumptions are right, your mouse is USB. If it gets "lost", unplug the mouse for ~3 seconds and plug it back in. It should work again, if only for a short period.
/L.A