Apparently I have a reputation of fixing things now!
Thanks for posting your workspace, Daniel. I can also confirm the issue. Basically what's happening is that when you click the bible reference, Accordance opens a new zone to display the chosen verses in. The bug/tweak needed is that due to Instant Details being on the bottom, Accordance tries to open it in a less-ideal location, so there isn't enough room to re-minimize everything. There are a couple of solutions here:
1) [Most ideal] Click on a verse reference when it isn't magnified, to have Accordance open your text window. Then, drag it somewhere nice and stable, perhaps as a tab somewhere in another zone, or in a small zone in a corner, or something. Now, when you click references, this tab will recycle, so everything should be good when re-minimizing it all.
2) Make your lexicon zone just a little wider. This will also help Accordance put the context zone in a little nicer place.
A couple of interesting things, though. FIrst, we'll take a look to see why the context is appearing in a less ideal location for minimizing. Second, the logic that occurs when closing the ESVS tab via Command-W is a bit funny with its error messages. Finally, we are also doing a bit funny logic for the closing of a zone/tab in magnify. So, we'll take a look at all this, thanks! It should be better for 10.1.5. In the meantime, I hope those workarounds help!