It's really annoying when that happens. On my netbook at home (win 7 starter), I have to keep moving stuff around to different ports to keep it working (these are just general things like usb drives, not being used with MC).
From searching around on the internet, the thing that seems most likely to me to be causing the trouble is the ports switching between usb1 and 2 improperly because of the existing uhci (or ohci depending on the chipset) controller drivers. From what I understand, the ECHI (usb2 controller) can do both USB2 and USB1 but the UHCI/OHCI controller messes it up by getting in the way when used with some devices. On my linux box, to avoid this, I remove the UHCI/OHCI drivers from the kernel. It doesn't look like you can do this in windows.
You might try microsoft update to see if there is an optional update to fix your usb issues, I have seen this referred to online when dealing with various chipsets. You might also check the MB manufacturers driver downloads to see if there is an updated driver for your machine.