Hi
I had exactly the same problem myself. Upgraded to s2member v131126, and s2member disappeared completely from the dashboard, but I could see the directories on the server.
Found your post and confirmed that I had the same issue – s2member.php was being removed from the server immediately on upload. Following some technical input from s2member support I raised a support ticket with my ISP who confirmed that they have an automatic scanner that inspects all files uploaded to their web servers.
The scanning software was adding the file to quarantine because it contained a symlink. They have now sorted this out (I dont have further details) but the file now uploads OK, and s2member is working again fine.
Hope this is some help