Service Advisory from Canon regarding the Canon 5D MKII Shutter Count
The shutter reading in the General Page of the software can be inaccurate by up to 2048 shots. This is the camera’s Internal Shutter Count.
The 5D II has a firmware bug that limits the accuracy of its shot count and total count, read or written, to within 2048 of the actual value. Since the internal shutter count was never designed to display its count to the user, it doesn't have much effect on them until they come in for service. Because of that Canon did not feel it necessary for an update to correct this defect.
You can verify the shutter count:
SPT software are definitely reading and writing the count correctly. We have been able to verify this by comparing to the camera's own built-in shutter count, accessible under the factory menu (DATA CK > ERR), which gives exactly the same results as the SPT Software.
The EOS 5d II stores the correct count until it gets above intervals of 2048 (800 in hexadecimal). Then it just fails to write the current count to Eeprom, until it gets to the next interval, which is 4092, and so on. It updates an internal counter, so the camera is able to maintain a shutter count, and if you click the shutter enough times, it will start reading correctly again (It'll just jump up by 2048).
Keep checking for Firmware Upgrades, Canon may address this issue at some point.