Thanks to your suggestions Clark I found out that it has to do with the USB hub on the keyboard. When booted up with the option key, no power to the ports on the keyboard. When the OS is booted up then the mouse works fine. Something to do with the resetting of the USB ports. Somehow going through it twice produces power at the ports on the keyboard. In any case the keyboard hub is "bad" in some way - it worked fine for about three months and then this just started up a couple of days ago. Final workaround is to just plug the mouse into it's own motherboard port and it works fine.
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