tibernut

I had a similar problem. I wasn't as far as Duna, I've experienced this in Kerbin orbit and on the Mun. Both times it happened to me I was able to regain control of the staged craft by toggling the antenna deployment off and on. In my case I only had 1 antenna. I wonder if you try to retract both antennas and then deploy them both if that would work for you. Its been a few days but I seem to remember that staging, then deploying the antennas worked for me also.