To reproduce:
1. Open any project
2. Click on an item in the hierarchy to highlight it. (Or anything else on the screen, to make the screen look different)
Notice that the screen still looks the same. Notice that it is possible to get it to refresh by changing the layout either by loading a preset, or by resizing a tab.

After a few seconds to a minute pass, these errors appear on the console:

Error while reading window layout: no main window found
UnityEditor.WindowLayout:LoadWindowLayout(String, Boolean)

Failed to load window layout: System.Exception: Exception of type 'System.Exception' was thrown.
at UnityEditor.WindowLayout.LoadWindowLayout (System.String path, Boolean newProjectLayoutWasCreated) [0x0031a] in /Users/builduser/buildslave/unity/build/Editor/Mono/GUI/WindowLayout.cs:574
UnityEditor.WindowLayout:LoadWindowLayout(String, Boolean)

Afterwards, the editor starts to behave normally.

The issue appears to be more noticeable with bigger projects, and only when opening a project that was last opened in a differrent version.