Yes, I was also starting to think that maybe the defrag tool was running when the error first appeared, but I looked at the scheduler and it says that defrag happens on Wednesdays at 01:00 AM, and this error first appeared on Sunday morning, and then never went away.
Having altered the timing (because of improved disk performance) maybe I had exposed a bug in one of the Windows services in the Windows guest. The app logs I looked at showed failures at different points though.
I know that VMware Workstation 6.5 shouldn't be sensitive to the fragmentation state of the vmdk, but I suppose it may also be possible it exposed a bug in VMware?