Comment 2 for bug 1359776

You could try out to manually create a new encfs config with standard settings but filename encoding set to stream.

From 'man encfs':

Filename Encoding
           New in 1.1. A choice is given between stream encoding of filename and block encoding.
           The advantage of stream encoding is that the encoded filenames will be as
           short as possible. If you have a filename with a single letter, it will be very short in the
           encoded form, where as block encoded filenames are always rounded
           up to the block size of the encryption cipher (8 bytes for Blowfish and 16 bytes for AES).

           The advantage of block encoding mode is that filename lenths all come out as a multiple
           of the cipher block size. This means that someone looking at your
           encrypted data can't tell as much about the length of your filenames. It is on by default,
           as it takes a similar amount of time to using the stream cipher.
           However stream cipher mode may be useful if you want shorter encrypted filenames for
           some reason.

           Prior to version 1.1, only stream encoding was supported.