Mark & all,
This is a general problem with Windows - we have the same problem as this, but the devices are weigh scales that transmit data over serial ports.
I must emphasize to Microsoft that this is NOT a device specific problem - the O/S will detect incoming serial data on system startup, and will "decide" that there is a mouse on that port. All that is needed is a systematic, well-documented method to prevent that from happening.
Mark - please contact me if you have any questions about this. This is an issue I & the company I work for have a lot of experience with!