Ah, for performance reasons I disable sorting when there is 1000+ files in the folder
You can change the limit by changing TotalFinderFoldersOnTopSortingLimit in
~/Library/Preferences/com.apple.finder.plist
Execute this line in Terminal.app and then restart Finder+TotalFinder:
defaults write com.apple.finder TotalFinderFoldersOnTopSortingLimit 1000000
I should indicate this visually somehow as an overlay on top of the view or something. Adding to my TODO list.