[robespierre]

You need to use single-user mode (runlevel s) to get a terminal without using the mouse. Unix requires this mode for many system maintenance tasks.
The mouse protocol is not in a file or a script, it is written into the kernel itself. You said that the problem happens when you boot from your new drive, which means that the drive has its own copy of the kernel. Each copy of the kernel has systune parameters inside it.

The situation could be the opposite way, where your accustomed boot disks are set for mice with a scroll wheel and the new disk is not.
I actually don't understand why you boot from different drives. Why don't you just create a single root (bootable) drive and mount more storage from there if you require it?