I have a similar problem. I didn't see your post, but I removed the deeplearning clone and went to reinstall and it looked like all of the "installed" modules were still installed..When I redid the clone, my problem still persists.
Did you actually "uninstall" the various Python packages? It seems like the ones I have are correct based on the instructions.
Here is my post: https://community.esri.com/thread/248776-train-deep-learning-model-not-recognizing-training-folders
Let me know if you or anyone has any other suggestions. I have not done anything differently than use the provided instructions both for the Python install and the steps to work on swimming pool ESRI example data.
Thank you,
Nate