I'm having the exact same problems in the last few days since the superdrive or EFI firmware update I believe. No amount of messing with the double click speed or tracking speed seems to help, as other threads have suggested.
I've tried to disable all the input manager extensions I have: multiclutch, SIMBL, SAFT, Typeit4me, but doesn't seem to help, and neither did a reboot.
Please help apple! this is truly aggravating and with the number of complainers in other threads (strangely marked "resolved" despite not clear resolution), obviously not an isolated issue.