If the OP's problem is anything like mine, then when I get the "modal" dialog box (as above) prompting to update - which appears as soon as Skype runs - I am unable to access Preferences since the option is simply greyed out (as well as all other options for that matter)! The only options I seem to have available are to "Force Quite" or [Download Now]!?
Also, the version of Skype that is offered as a "new version" is version 6.3 - this is not the latest version!? Yet, I have OS 10.6.8, which reportedly supports the latest version of Skype (according to the above system requirements)!?