FWIW there is a workaround that lets Box.net work with BoxCryptor in Windows and in the BoxCryptor Android app. The following worked for me with a Boxcryptor folder created via the instructions linked from Robert's post. Boxcryptor's Android app happily recognized the resulting folder and let me upload/edit encrypted files that synced to my Windows PC.
The issue is Box.net's inability to sync files beginning with a dot. I.e. the locally-created configuration file won't upload to Box. Consequently BoxCryptor on another PC (or in Android) won't recognize the BoxCryptor folder in Box. Robert's linked instructions provide for renaming the configuration file, but BoxCryptor's android app doesn't currently recognize anything but the default name.
Box seems to have no problem with storing files with names that start with a dot -- once you get them to Box's server.
Solution: Make a copy of your locally-created ".encfs6.xml" file and change the name by deleting the dot. Upload that to the Boxcryptor folder and then use Box's web interface to change the file name by adding back the dot.