Panelizer Content Page not reflecting layout changes

Having recently updated to Panopoly 1.38 there was a security bulletin on Panelizer and Panels so we decided to update these modules independently of the distro and updated Panelizer, CTools and Panels as follows:

CTools 1.9 -> 1.10

Panels 3.5 -> 3.7

Panelizer 3.1 -> 3.4

After this update we experienced two problems. The first was that we were getting an Access Denied error when attempting to add new panes to a layout. See: https://www.drupal.org/node/2785945 Updating Panelizer to the latest dev release fixed this issue. The second issue is that we are unable to change the layout for any Panelizer configured view mode. If we do so the edit content screen shows the old layout still.

We discovered a way to get our layouts to work again, though it is hardly ideal. Without looking at the content of a given layout in Panelizer (reasons below), if we select the layouts page first and then save the layout again (each time it is required that we choose a different layout even when a correctly selected AT Layout is shown, for instance), then move the contents to the relevant panes and finally reach the content page, everything works fine. The key to the fix here is saving the layout first.

If the content page is accessed in Panelizer before saving a layout the Panelizer content page is effectively broken from that point. The reasons for this is that in the case of not saving a layout first, when accessing the content page a record is added to ctools_object_cache table. If we now chose a different layout, move the panes and return to the content page the layout will not have changed to the new choice. If we then delete the record from the ctools_object_cache table and refresh the content page, the layout shows the newly selected version and from that point everything works fine for that view mode. No new record is added to ctools_object_cache.

Both patches from https://www.drupal.org/node/2785945 have been run and reported back that nothing had been changed.

We manage our site using Features and Jenkins deployments and have discovered that since the update all our layout features show as overridden and these features do not revert. If we change the layout using the technique above, and resave the features, without reverting they immediately show as not overridden on deployment but the issue itself has not been fixed. i.e. we are still not able to modify the layout.

Thank you in advance for any advice or help with this problem.