The tree is rebuilt on each refresh, but it often displays unneeded items for a short period of time first, and only then it gets updated to the normal state. This results in a small visual glitch, which would be nice to get rid of.
Slowmo:
The set of temporarily shown duplicates is dynamic, may consist of folders from Favorites, or folders like 'Desktop', 'Pictures' etc.
Upd: Better example (slowmo):
The scale of glitch seems to depend on the folder which is opened in lister.
Indeed, glitch disappeared in 13.0.46! At least when casually refreshing. When I spam that command I still see a little of artifacts, but this is no way compares to what was before and is not a problem at all. Thanks!
Found something more about this. Folder Tree gets glitched again if I turn off 'Animate controls and elements inside windows' in System -> Performance options:
