This had be stumped for a moment as i have never encountered this before. The following knowledge base by VMware explains this behaviour and how to overcome.
Luckily I was in the position to power of the virtual machine and download the VMX file and power back on. Though when I tried again with the virtual machine powered back on, same issue occurred.
I did find when vMotioning between hosts (same datastore) I could then download the VMX file with the virtual machine still on.
I have read that similar people have had issues with brackets in the virtual machine name (wasn’t the case here) that can get confused with the datastores (as brackets define datastores). Might be worth watching out for this one.
This was using VMware ESXi 5.0.0 768111.