I just noticed this thread, I apologize for the delay.
If the pages load fine, but the settings are gone, it may be that you didn't enable the deactivation safeguards before updating.
WP Admin -> s2Member -> General Options -> Deactivation Safeguards.
This thread gives a good way to update your plugin by hand if the auto-update didn't work for some reason:
viewtopic.php?f=36&t=247And if the problem is that your settings pages aren't loading fine after checking the above, like when you get an empty settings page, it may be a JavaScript issue explained here:
http://www.s2member.com/options-page-di ... ing-video/Let me know if that helps.