I didn't put this in the suggestion forum since (1) this is so obvious and (2) I use Libronix but I thought SURELY they'd have fixed this in Logos4 (don't know about Logos5; I absolutely refuse to upgrade just to see if they fixed it).
For example, if you have a DSS Biblical resource open and linked to your Bible study, every time you jump to a new book, Logos4 (or L5??) jumps to the desired new resource. But completely ignores your settings (font size, whether TOC open, etc).
So I dutifully reset it each time. This wouldn't normally be such a problem for commentaries etc. Over time, you could reset all 66 books for each commentary.
But for the DSS Biblical resources, Gottingen, targums and NT papyri, it's a super headache. There's more than 66 each.
Now, admittedly ... as a Libronix user, it's the SAME headache. So maybe no need to fix ... I've not seen anyone else with this issue.