Please provide additional information.
How big is the compact flash memory? What system is it being used on? Is it the same size memory as the original?
What command line switches did you use to create the original image? What command line switches did you use to restore the image? Is the CF formatted FAT32 or NTFS ?
How did you clone the disk? If you cloned it on another system then that might be the reason for your problems.
Does your flash memory have only one partition? Is there any possibility that the system may have any part of the bios on the flash memory?