I have a Saved Layout that has two windows. It was saved in the state where each window was on one of my two monitors. When I load this layout, the window that was on the second monitor when the layout was saved is opened on the main monitor instead, behind the window that is supposed to be there. This appears to be new with v7; I don't recall seeing this problem in v6, and I've been using saved layouts like this for quite some time. The behavior is consistent for new layouts and old layouts, and whether the layout is loaded explicitly from the Layouts menu or by restarting Logos.
I am using Logos 7.2 SR-1 (7.2.0.0038), Bronze edition. My computer is an Apple iMac 27 in. late 2013 running macOS Sierra (v10.12.1) with 16GB RAM. The main monitor is the built-in monitor, the secondary monitor is an Acer AL2216W.