Tonight I upgraded one of my sites from 3.2.1 to 3.3.2. After that, my site was running fine (complete SSL on every page per usual). Then I upgraded the HTTPS (SSL) plugin from 1.9.2 to 3.0.2 and my menus link to http:// pages instead of https:// and a lot of my images stopped using the https:// prefix as well.
Downgrading back to 1.9.2 fixed my issues. Looks like 3.0.2 is missing the Internal HTTPS Elements option (from the change log it looks like it's supposed to tag them all by default in 3.0.2).