Perhaps the scanner's sucking too much power off the bus? I mean...if I understand you correctly, you've got the scanner plugged directly into the machine, but maybe that's just too much of a drain on the bus. <shrugs>
Have you tried disconnecting the scanner and testing the mouse through the keyboard? Make sure you try both USB ports on the keyboard when you do this. What machine are you using this on? You aren't using a 3rd party USB PCI card, are you? I've got that same mouse (it's great!) and it works just fine going through my G4 keyboard (yes, I know...) that's hooked up to my B&W G3. If all else fails, I'd first exchange the mouse for another just like it and if that doesn't help, either switch to a different model mouse or try/buy a powered hub. Good luck.