In folder view I see:
ProgramData
Document and Setings
Recovery
System Volume information
I don't see them in the listers. (hide hidden files is off)
How can I make all files visible in the listers?
Turn off hide system files as well.
Both are off (in preferences - Folders - Folder display)
Everything is off like in your picture 
I'm using this theme: KingOfDaClick's Pack 2018 - (.ocb file only)
When I select another theme all is fine.
That isn't just a theme, it's an entire config. Who knows what settings it might change. 
Yeah you are right about that 
Does Opus override all settings in Windows? If not; perhaps something in Windows needs to be configured.
For example when I access this PC from my other PC over my LAN it keeps ignoring access system folders.
Could it be a Windows security setting that stops Opus looking at those directories?
BTW I can see every hidden (system) file with the regular Windows Explorer.
If it was file permissions I think it would affect everything below c:\ so I don't think it's that.
Do the folders show up in Explorer?
[quote="leo"]Do the folders show up in Explorer?[/quote]Yes in the standard Windows Explorer everything shows up.
Hidden files also show up in Opus tree view.
But as said no in the main listers. When I enter "C:\ProgramData" in the file path box the hidden folder does open.
The tree view shows 12 hidden (red) sub-folders. The main lister shows just one "Microsoft". It opens when I click it.
It gets even weirder. I just restored my previous settings. Those are very basic. No extra icon/theme sets. Just standard stuff.
Guess what.... in tree view the hidden files are hidden and in the main list they are visible. That's just the other way around. 
Nothing mysterious there. Your old settings must have the tree configured to hide hidden and/or system files. 