I had to temporarely encrypt some folders since I wanted to test the performance of different sftp clients.
And working on the fly within the "container" is not really recommended when you are using plenty of small files.
At least 2-3 years ago it was the case and I never had time to test it again. I just gave up that time.
Out of interest - do you compile Boxcryptor within of an encrypted folder or in a standard one?