Why does OS X keep forgetting my trackpad settings
The symptoms you describe are caused by the preference not getting saved to disk. Sometimes the cause is that there is a problem with the file permissions (as per thaatz's answer).
Another possibility is that the preference file somehow got corrupted; if this is the case, you can move the preference file (I think the relevant one is ~/Library/Preferences/com.apple.driver.AppleBluetoothMultitouch.trackpad.plist) from its location: this will cause the preference file to be recreated.
Of course this will work also for other preferences (though identifying the correct file isn't always as easy); remember to keep the file around (instead of deleting it) so you can restore it in case this fix doesn't work.