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I don't remember exactly when USB became standard on Mac hardware, but I think it was quite a bit after OS X came out.
USB appeared in the Bondi Blue (first) iMacs in 1998, well before OS X debuted.
However, OS 9 does handle USB differently than OS X (extensions and whatnot) so there may be something going on there. I'm afraid that OS 9 has become the distant past for me...I haven't used it at home for almost 10 years and last used it at the newspaper over 5 years ago and there wasn't much fiddling to be done with the OS etc. then.
Suspect that the extra steps off the main USB bus from the display is causing OS 9 to not recognize the attachments on boot. USB is a polled concept and requires the host to look for signals that something is attached. FW on the other hand can in a sense activate itself and act independently of a host controller. And USB is a shared pipe with the bandwidth divided among the devices sometimes needing a driver to initiate connectivity. In your case, uplugging and replugging the mouse signals the host that something needs attention. OSX is better programmed to look for those attachments beyond the basic bus.
I think. 
Here is a basic description of how the USB system works:
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Host Controller Driver
As a request for a data transfer moves from the device driver, through the USB Driver, and through the USB Hub Driver, the request gains all the information needed for the host controller to generate the appropriate transactions on the bus. However, depending on the host controller, this information needs to be formatted in a certain way and added for scheduling by the host controller.
This task if given to the host controller driver. Requests reach the host controller driver in a system-defined format, often called a USB Request Block (URB), or an I/O Request Packet (IRP).
Additionally, host controller drivers are loaded by the PCI subsystem when a corresponding host controller is discovered during PCI enumeration. The host controller driver is thus also responsible for initializing the host controller and perhaps loading the USB Hub Driver and the USB driver. Combined, the USB driver, USB hub driver, and the host controller driver make up a USB subsystem.
More:
http://wiki.osdev.org/USB
And more:
http://en.wikipedia.org/wiki/USB_2.0#USB_c...d_with_FireWire