Hi Charlie,
A little belated, but the broken site I mentioned in post Pro 6.6 Beta 1 - HTML Storage - Message for which storage engine we are using is still present in beta 2.
I created a staging site for the in-development site (see Secure Note). Although update to beta 2 from 6.5.15 the same misalignments were present as in beta 1 - please see before and after screenshots.
Official Release 6.5.15
Same Image After Beta 2 and HTML Conversion
Another page - With official release
With Beta 2 and Aftwer HTML Conversion
In all cases, please notice both the margins and height of sections.
More details in the secure note!
All best,
Christopher