I am using 6.2 SR-1 (6.2.0.0043) on Windows 8.1 and have noticed this behaviour for a while though I don't recall when I started to see it (and whether it was different before). First, the open note in an open note file often drops out of focus when one switches to other windows in Logos. In other words, if I was typing in the text body of a note, leave it open and then say check something in another window, when I return to it, it is often closed. But the second behaviour is also a bit odd: when the individual note, arranged to be at the top (as in "newest created first"), collapses in compact mode when I switch to another window, I find that the scroll indicator is afterward a bit lower than the top entry and I need to scroll up a bit in order to reopen it.
Although I have observed this several times, for some reason, I cannot reproduce it just now. So perhaps there is some other attendant factor that I need to make note of. Next time it happens, I will endeavor to observe more carefully these circumstances. In the meantime, others may be able to point out whether this is something they have experienced as well.