I realize this is probably not a very common configuration nor may it be supported, but here's the issue:
On Windows Server 2012, I have my boxcryptor (version 1.5) volume on an NTFS volume with block level deduplication enabled. I can mount the box cryptor volume and view the folder structure and file names, but I cannot view any files or copy them out of the encrypted volume, getting a "file not found" error. The same files open fine on my Android device (thankfully!). On the server I am able to add new files to the encrypted volume, and I am able to open them right away after I add them, presumably because they have not been deduplicated yet, as it is post-process not in-line deduplication.
Let me know if this is something you are willing to troubleshoot and I'll be willing to test some things if you are unable to replicate the environment. Thanks!
EDIT: Now that I think about it a bit more, I'm guessing that this probably could never work since the encrypted data deduplicates differently than the unencrypted data, so it would have to be duplicated (un-deduplicated, reduplicated?) before being decrypted. I'll plan on just moving it off the deduplicated file system, but I'm still curious if anybody has suggestions for how to resolve this problem. While I don't have a lot of encrypted data, it's synced with dropbox so I'll have to move my whole dropbox off the deduped volume since Dropbox still doesn't allow folders outside of the dropbox folder to be synced AFAIK.
EDIT2: Server 2012 allows you to exclude certain directories from being deduplicated. This should essentially solve my problem and I'll quit talking to myself now. Hopefully somebody will find this useful. I'm still curious as to how one would deal with the encryption/deduplication paradigm for large amounts of data.