The problem is that BoxCryptor uses a configuration file called .encfs6.xml which is located in the root of your BoxCryptor Folder (e.g. BoxCryptor.bc\.encfs6.xml). However, Cubby does not sync hidden files (files beginning with a dot are hidden files on Unix systems) according to this thread:
This causes the .encfs6.xml file to be missing on your second computer and thus BoxCryptor cannot open the folder. In order to circumvent this problem, simply rename the ".encfs6.xml" file to "Keyfile.bcx". As a fallback mechanism BoxCryptor looks for "Keyfile.bcx" if a ".encfs6.xml" file could not be found.