Where did this problem VM originate from - was it always a VM or has it been P2V'd? What hardware version is it?
Have you checked the disk alignment to ensure that it's not misaligned IO causing this performance degradation?
You can use this script to check disk alignment on Windows servers;
http://www.jonmunday.net/2013/03/20/are-all-your-guest-os-partition-correctly-aligned/
Perhaps running vcscistats will give you some insight into the IO characteristics.
Does performance stay the same regardless of which host you run it on?
What happens if you add a new disk to this VM at check performance of this disk - how does that compare?
Is performance the same if you create a new VM and attach these VMDK's?
This is an interesting one, and I'm looking forward to understanding what's causing this.
Cheers,
Jon