XYplorer Beta Club

No, it is normal Windows folders where i have changed the icons to custom ones. The folders are not a part of any 3rd party app.

So the icons are defined via Desktop.ini? I tested this case and cannot reproduce it here.

Yes exactly:
[.ShellClassInfo]
IconResource=C:\Icons\COMODO.ico,0

I don't understand why you can't reproduce it. It is very obvious and constant here.
I can add that Windows Explorer shows the icons correctly in both left and right pane.
Another note is that if I insert a usb harddrive, the folder icons don't change to correct ones. It must be a usb flash drive
This is absolutely not a big deal, but maybe related to the other usb flash insert trouble, seen in other threats.

Windows is full of mysteries. You seem to use Win 7, I use Win 8. That alone could account for thousands of different experiences.

Conc. the OT: The setting of "Configuration | Tree and List | Tree | Expand destination node in tree" also plays / played a role. Will be fixed in next version.

"v16.20.0203 - 2016-02-15 16:44
Configuration | Tree and List | Tree | Show localized folder names:
Special folder icons were not displayed in the tree with this setting enabled. Fixed".

That did the job