I've noticed this for a while now.
If I have the NIV2011 opened in a layout I loaded on startup, and I press F7 (to compare versions), nothing happens. If I switch out of the NIV2011 and then back, it will work.
Once it works, it always works (even if I change layouts).
I have not noticed this behavior with other Bibles.
[sigh]
And now, when I just restarted Logos to test the steps again, it's behaving as it should. But I really do see this happen from time to time. Honest! (If I get a little time, I may restart the computer and see if it's related to first time use after a restart.)