I'm having a similar problem using Photo Mechanic Version 6.0, build 3023 on a Mac, High Sierra 10.13.6
When creating a new folder in an external HD, a new & highlighted 'untitled folder' fails to show in the folder list. Instead, the highlight jumps to an already used, seemingly random, folder further down the list structure.
Looking at the ext HD in the Finder shows the Untitled folder has been created, and I can rename it, but it doesn't show in PM until PM is restarted. Refreshing PM doesn't update the navigator.
I can create a folder on the internal HD no problem, but not sure what the issue is.
Any ideas gratefully received.