There’s a long-time Windows Scriv bug, from beta days, where launching Composition Mode on the main editor will arbitrarily reposition open Quick Ref windows.
My workaround for the Scriv bug has been to enable Window > Float Quick Ref Panels. For whatever reason, when this setting is enabled, Comp Mode no longer repositions the Quick Ref windows.
I have dual monitors, and a frequent setup I use is Comp Mode in the left monitor and Quick Ref panels with research and notes on the right monitor. I must keep Window > Float Quick Ref Panels enabled for this setup to work, otherwise every time I launch Comp Mode the Quick Ref panels get moved around.
It’s lame, but it is what it is. My assumption is this must be a tricky or impossible bug to fix, otherwise it would have been fixed long ago.