New SSL installed - permalinks not working anymore

I followed the 2 blog posts on this site about setting up SSL and then adding the Domain Mapping, but now my permalinks are not working on both the main site or the multisite(s). I changed them to "plain/default" and they worked, but then I get an error message saying Membership2 won't work like that. who wants to use those ugly permalinks? Not I!

What am I missing? What can I do to fix this?