Ok now I have read through all this from the perspective of a non vista user.
Accepting everything that you say, Vista has incorporated an improved sleep mode as part of its normal setup. Knowing that, It just seems unusual that the problems that were solved by disconnecting certain peripherals should have happened in the first place. I am sure that Vista does not suggest that you detach every usb device for sleep mode to function.
Dirty Polo has gone through most, if not all, of the obscure settings that may have been involved in your issue without success. I agree that disconnecting would have the same effect as removing the batteries but if it works, it may still be more than just the mouse,, etc.
Something odd is going on with your usb ports and it may well be hardware related.