All CORE theme's are being styled from base/style/core.css, so this alignment problem will be affecting ALL themes in master, and so will need fixing in BASE theme.
I don't think the original fix was added to MOODLE_22_STABLE, so that's probably why the login looks ok.
If this gets passed as it is, I can fix the footer as a sub-task of this issue, and fix BASE as a sub-task of
MDL-29724 which was where I did the original fix for all CORE themes. And have both ready for next week.
Otherwise FAIL this and I'll fix the lot next week.