A number of issues were found in the cryptography practices of EncFS. These are detailed in the following audit:
https://defuse.ca/audits/encfs.htm
It also notes some of the issues in bug 630460 may not be fixed correctly.
A fix is currently not available. Fedora and EPEL use a 1.x version. A future 2.0 release may correct these issues: https://code.google.com/p/encfs/issues/detail?id=186