you will probably need to change the mouse protocol being used by X. Different mice send different signals for different clicks, and the protocol allows X to figure out which signal corresponds to each type of click. So it sounds as if you have the wrong one. Unfortunately, I don't know which protocol is the right one. But you can change it by adding the line
Option "Protocol" "protocol_name"
to the mouse section of xorg.conf.
Most mice I've used use either the IMPS/2 or the ExplorerPS/2 protocol. You can find a list of protocols in the "mouse" man page.