USB mice/trackballs have two different protocols they can operate in: Boot 
Protocol and Report Protocol.  In Boot Protocol, the mouse is supposed to 
emulate a standard PS2 mouse, and use the protocol as you describe it.  In 
Report Mode, the mouse can operate any way it wants to, but must describe how 
it works with a USB HID Report Descriptor.

When a USB mouse first initializes, it comes up in Report Protocol rather than 
Boot Protocol (exactly backwards from what you would expect it to do).  If the 
BIOS doesn't want to download the Report Descriptor to figure out how the mouse 
is actually designed to work, it must tell the mouse to switch to Boot Protocol.

Like many devices in the USB world, unfortunately, some mice/trackballs do not 
follow the standards.  So, even if your BIOS is telling the mouse to change to 
Boot Protocol (which the BIOS may not even be doing), the mouse may simply 
ignore the BIOS and stay in Report Protocol.

While modifying CTMOUSE is certainly an option, it is probably not the best 
route to take.  If your USB controller is UHCI, you can try my USB drivers 
(available at http://bretjohnson.us).  I can't guarantee it will work with your 
particular trackball, but if it does it is probably a better option than 
rewriting CTMOUSE.

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