Well, Converter transfers the content of vmdks as it is using disklib. You mentioned there are no snapshots on the source, but can you double check it? Pardon me if that sounds stupid, but that's the only thing I can think of to cause such an issue.
If the source machine has snapshots, Converter copies the current state. So, if somehow it has been reverted to some old one, it will copy the old data. Perhaps, if something has gone wrong with the snapshot tree, this could also happen (just speculating)
Regards
Plamen