Hi, sounds strange.
I use BC mainly on google drive, iCloud and dropbox and it syncs with two iOS devices and two macs close to perfection.
The first case I had only once: A file stored on my iPad did not show up anywhere else. Deleted the file on my iPad, re-stored it again. That solved the issue. Happened never again.
Some years ago I had the case, that I could not open an specific document out of boxcryptor's virtual drive on a mac; copying of the file to my desktop solved the issue. I guess, that some metadata were not available in the BC drive copy. But all that happened years ago.
Sorry; can't help you any better.