Ran some other tests and found out that several conditions keep to all broken icons:
- Only happens in folder portals.
- All files with broken icons are shortcuts.
- Shortcuts lead to some .exe file, not an .ico file.
- That .exe file has library with several (more than one) icons inside.
So, I extracted icons from executables using some other software, and linked shortcuts directly to that icons. However, it is quite uncomfortable. Hope this will be fixed in future versions.