When a remote home folder is used with Active Directory, you may notice file and/or directories suddenly and unexpectedly disappear and then reappear later only to eventually disappear again.  This problem is caused by OS X having difficulty maintaining its connection to the remote home directory through Windows file sharing.  OS X has had severe problems with Windows file sharing since version 10.7.  A work around is currently being developed by Aqua Connect but is not yet complete.

Due to the severe bugs in OS X for Windows file sharing, Aqua Connect recommends that users not use remote home folders with Active Directory at this time.

See also: https://discussions.apple.com/thread/5295907?tstart=0
See also: http://www.tweaking4all.com/os-tips-and-tricks/macosx-tips-and-tricks/smbup-mac-os-x-smb-fix/