Something is forcing MIME to CD conversion on your MIME messages (I know you have "Keep in sender's format"). Prove this by attempting to look at the raw MIME source of a sample message (View / Show / Page Source) - this will be greyed out because there is no MIME source to look at.
Likely culprit is your virus scanner.
We had this issue a long while back when first starting to use native MIME in R5. Can't remember what virus scanner it was but it could only check CD messages and so the hook that grabbed the messages in mail.box forced a MIME to CD conversion on every MIME message received regardless of the users' preferences.
Our current virus checker preserves the native MIME of all MIME messages (even when quarantining viruses which is useful in some cases where the MIME is deliberately malformed).
You could try looking for settings in the virus scanner to see whether it has the option to preserve MIME.
HTH
Chris Linfoot
http://chris-linfoot.net