I think you are synchronizing your eBooks with the Cybook, if so you have two choices to resolve your problem:
1 - open the windows mobipocket reader, choose in the left the icon devices and choose Edit properties from the Cybook Gen3 device. From the window that appears choose Synchronization, and see what it’s chosen for the option “When I send an eBook to this handheld, copy it to:”, if it’s activated for “Card” or “Best location” change it to “Main memory”;
2 - when you connect your Cybook to your PC it is seen by it as a new drive Called “Cybook”, just copy your eBooks with (per example windows explorer) to that drive, into the eBooks folder.
Hope this helps.