I just started working on a couple of new sites and have noticed that it appears that Layouts and / or Layouts Genesis Integration plugin messes up the HTML structure on Genesis v 2.4.2.
Here's the basic high level structure of a default Genesis installation:
site-container
header
nav
site-inner
content-sidebar-wrap
main.content
aside.sidebar
footer
And here's the structure with Layouts and Layouts Genesis Integration plugins active:
site-container
site-inner
content-sidebar-wrap
main.content
header
nav
footer
aside.sidebar
As you can see, it's nesting the header, footer, and aside.sidebar within main.content and forcing the aside.sidebar to its own row below the footer.
The aside.sidebar is inserted automatically on a row of its own even on a new installation I just started that is using a Layout for a page but has no cells assigned to it.
I have confirmed this problem on multiple installations running Layouts and Layouts Genesis Integration plugins and Genesis v 2.4.2.
I do have one installation running Genesis 2.3.1 where the structure is correct, so it appears that somewhere between 2.3.1 and 2.4.2 there is a problem.
Our compatibility team have been working on further updates to the integration plugin to accommodate the changes in Genesis 2.4 in response to client feedback, and will publish an update soon.
That update modifies the CSS. You can get the updated theme-integration.css file here to test for yourself: hidden link
You will need to overwrite the existing file at /wp-content/plugins/layouts-genesis/public/css/theme-integration.css
It would be helpful if you could check and report back.
I note that your initial comment describes differences in the markup structure rather than the CSS and so in the meantime I'm going to pass that info on to our developers.
Let me pre-empt any more testing on your part by confirming that the devs are working on the structural markup changes, too, and this is still in progress.
I am escalating this thread so I can add it to the relevant internal ticket for tracking and will keep you posted with developments.
You may have noticed we pushed out some updates overnight, but these were minor 'hotfixes' in preparation for the release of WordPress 4.7 next week.
Testing is now underway on the full batch of releases which will include Layouts 1.9. The integration plugin updates—including the Genesis integration which contains the fix for the existing issues—will be published at the same time, so that testing can confirm that no new issues relating to Layouts 1.9 appear.
We expect to be ready with the updates, all being well, in a couple of weeks.
I'm just reviewing the tickets marked as fixed in next release in anticipation of a slew of updates for the main Toolset plugins intended to be published after the weekend when testing is completed.
The Genesis integration plugin has been pending, waiting on the release of Layouts 1.9 which was a major update, and both will be published next week. That should hopefully resolve your issue.