Okay, so I did some more comparison.
I have another Zotac mini-pc that's running Kodibuntu. Previously I just used it as a thin client with all the setup being done from my windows machine, but I went and tested it.
I added the same network path to it as is added to Kodi on my Windows machine, then went to Files view on both Windows Machine and Kodibuntu. They should match given they both have the same permissions, but they don't...
Windows Machine
Kodibuntu
The Kodibuntu machine is seeing all the directories that are actually there. The Kodi installed on Windows continues to not see some directories, despite File Explorer on the same machine being able to see everything.
Quality sucks, but this shows how opening the Movies shared folder on my Windows machine (on same machine Kodi is having issues on), causes some folders to show up first, then others afterwards.
https://goo.gl/photos/ef3AZocnfDzM6vGi8