Hi ellblud,
What image are you on and how are you transferring the settings onto the Duo?
If you are on Vix 2.3 (Linux 3.1.1) and you are using DreamBoxEdit to transfer your settings make sure that you have updated the port on the Duo or DreamBoxEdit to match. On the latest image the default port is set to 8080 where as it used be just 80. The settings will not 100% successfully transfer onto the Duo from DBE if the port is not correct.
If you are taking the latest settings directly from the feeds then I'm not sure why this is happening. Is the box rebooting after you uploaded the settings?
Cheers,
mcquaim