Make sure you do not have any specific rules set up that are possibly placing the icons on and alternate Desktop Page (Fences config, Sorting / organizing). Also, you might want to try restoring to a previous 'snapshot' to see if this resolves your issue.
http://sd.stardock.com/sean/jingimages/2013-05-14_0817.png
Worst case, you can, on the same config menu, 'Perform automatic layout'.
If this fails, please place a support ticket at support@stardock.com
