Ok. Thanks all. Cracked it. The Macally driver was indeed the culprit. I had installed it way back in OSX 10.1 or maybe before that even when the standard Apple driver did nothing for my scroll wheel etc. I had just kept updating it thinking it was needed. Just run the uninstaller (which you can get by downloading from http://www.macally.com/techsupport/drivers.html ) in case, like me, you had ditched it. A system reboot is needed.
In 10.2.1 at least all Macally mouse functions are supported by the Apple driver and proper 3 button control is present in PyMOL. :-) Uninstall seems to be the only option as the Macally utility for customising what the buttons do on an application by application basis does not include an option of excluding an application such as PyMOL. Correct me if I missed something though. :-( -- .-Dr-Andy-Calder----------. | Materials Modelling Group\ | Materials Science & Eng. \ | University of Liverpool / | UK .---------------------'