Hard Drive Capacity Confusion

http://en.wikipedia.org/wiki/System_file

The files appear to be corrupted.

however, there is another scenario… have you recently deleted files from the old 500 gb drive?

the mac will still reflect those files as been on the hd even when you have drag then to the garbage bin.

if that’s not the case run first aid on both drives using disk utilities 

remember that this is a hypothesis and does not mean it has to be one of the two… but lest start with this assumption and see what else we can do