Recently got that programme and wrote to Acronis about one or two things. They took about a week to get back to me but were then very helpful.
I've got two separate images in the Secure Zone and have defragmented a few times with Diskeeper. The Secure Zone isn't affected as only the c partition is defragmented. (I only have the one partition).
I've verified the images twice over the last week just to make sure. If you look in Computer Manangement/Disk Manangement (on XP) you'll see the Secure Zone as a separate partition. i.e you don't have to delete the Secure Zone before you defragment the rest of your drive.
In my inital toings and froings with the programme I deleted the Secure Zone and allocated the space back to the c partition. It gave back every last mb so you should definitely not be losing disk space. I hope you get a satisfactory explanation from them.
(PS. I've taken so long writing this I bet, meantime, someone has answered your query and you've ticked it as resolved).