Command "Go REFRESH=ALL" sometimes doesn't refresh both listers, only selected.
Any pattern to it, like which (kind of) directory is in either side, or the tree being on/off or something?
How are you triggering the refresh? Toolbar/menu or hotkey?
No tree, only dual view, using "F5".
I have activated option "newer files at the end" (but this should only affect automatic referesh).
I turned on the option and set my F5 to run the same command, then pushed it over and over with various combinations of folders but it always seemed to refresh for me. (As in, I could see each side briefly clear and then re-appear.)
Can you make it happen like that or does it only occur every so often?
Okay, it's "F5"
When using only active listers refreshes. If using button, both refreshes.
Maybe I have to check keybinding?
That would be sensible. Use Settings -> Customize -> Keys to find out what it's running.
Ohh noooo!!!!!!!!
Keybinding was "refresh=source"! 
Is this by default (because I never changed this)?
The default is Go REFRESH=source, which comes from the View->Refresh item in the default menus (which has F5 as a hotkey).