Yes, I would too, asking questions to get a complete picture of steps taken to get to this. So far I am unable to reproduce. Changes I make to the window layout stick without explicitly saving the last layout I had opened.
@AMG please run the Rhino command _SystemInfo and paste the complete result here in a reply.
To mitigate this issue I have added a startup macro (_-WindowLayout Minimal _Enter) for my custom window layout Minimal.rhw (29.4 KB), but even then I still have some toolbars open and visible after I restart the Rhino application.
I see the problem of your second video when using the startup command -WindowLayout where there is a floating container until you click in Rhino. But I am unable to reproduce the behavior from your first video.
Logged the second issue as RH-82447 Left container pops up on -WindowLayout
Tested with two different layouts, Minimal.rhw (29.4 KB) and Minimal 2.rhw (29.6 KB). When using the former the window layout do not persist, but when using the latter the window layout do persist between sessions.