Only a guess. Can you confirm the source .vmdk shows the correct size of the RDM? In case the raw LUN has been resized after the RDM was created, the size information in the .vmdk header file may not match the real LUN size and therefore the vmkfstools command will not copy all data. In case of an MBR partition you will be "just" missing data, but in case of a GPT partition table you might be missing the protective header/table.
André