I still keep having the same two problems. More often than not closing PhpED only closes the workspace (even if I wait, so it's not that I'm not patient).

Cloned windows more often than not don't get saved so after closing PhpED and opening it again I have to add my cloned windows again because they're gone.

Something similar to this was fixed in 5028 or 5029.

I only just realised there's a 5029 build (I was still on 5025).

I've installed it and so far so good.
I tried opening closing a couple of times and no problem.