Wim,
Please keep us updated on this issue! I am also having the problem where i have multiple monitors connected to a GTX 680 in Windows 7 x64 as well as a 10" displaylink monitor. When I connect the displaylink monitor I loose all the settings in my Nvidia control panel except for 3D settings.
looks exactly like the photos in this thread
here
Definitely sounds like you will need to work with Nvidia to get this resolved, I get the impression this is an unintended Nvidia "feature" as you described earlier.
Appreciate that this is actively being looked into.