4 months ago I noticed the problem on my MAC. See topic: https://forums.boxcryptor.com/topic/some-folders-are-not-shown-on-mac
Now I can reproduce the same issue even on one of my Windows PC.
After some investigation, I narrowed down the problem.
Only folder with specific name will be "missing".
If I create a folder with name "存 -", it can't be displayed in boxcryptor.
Please note the first character is Chinese "存" the second one is ascii space and third one is ascii minus.
This specific name is the only problematic one I can found. There might be others. Anyway, this looks to me a dangerous bug.