Definitely try booting from a floppy or CD just to verify for sure that it's not the OS doing it. If that's not easily available, take the back cover off, unplug the hard drive, turn on the Mac, and try moving the mouse when you see the question mark / disk icon. Also try unplugging the keyboard and attaching the mouse directly after you turn it on. As mentioned, it's not too bad to hot-plug those cables, especially if you have a good reason to do it.

These are just easy, harmless things to try that could maybe provide useful clues before you get out the soldering iron.