I don't know why SW isn't remembering the setting, but till you find an answer you could save/export the registry key at HKEY_CURRENT_USER > Software > Solidworks > SolidWorks 2012 > User Interface > Settings > Mouse Gestures and simply double click to re-install each time.
It's possible you are crashing or the application isn't closing properly each night. Try starting up SolidWorks, set up your mouse gestures and then close SolidWorks without doing anything else... This will force everything to get cleanly written to the registry. From there on out, it should work without a hitch.
Keeping a backup as Kelvin suggests is a good idea too. You can do it directly as he suggests above or save a copy using the "SolidWorks - SolidWorks Tools - Copy Settings Wizard" found on your system "Start" menu...
Message was edited by: John Sweeney
I will try both of these options. It was just an odd scenario. What I found even more odd was that I had set up a keyboard short cut for the measure tool and that has never disappeared. So I may make a phone call to my IT dept and have them do a clean install as we just updated to 2012 a few weeks ago.
It sounds as if something is triggering "reset to defaults" before closing SW.