To suppress the display of system files (configuration files, those that start with a dot) when connecting from a Windows computer to your samba server, write the following into the /etc/samba/smb.conf:
hide dot files = yes
I tested the encrypted file sharing application KDX under wine. It works perfectly. I wonder why it isn't on the wine gold list. The reason why it works so well is that it doesn't rely heavily on the windows base, but does most of the needed stuff (graphics, etc.) itself: KDXClient1110-Win.zip. BTW: I used as a tracker hlsux.bugdave.com.