I had this problem as well with Windows XP. What I found is that my manually created disk had an entry for independent-persistent mode. I had to comment out this line in the VM's vmx config file to gain snapshot capability.
#scsi0:0.mode = "independent-persistent"
(revised for accuracy)
Well your suggestion, at least made me go have a delve through my rather sprawling .vmx file which has gone through workstation and server before ending up in fusion.
And sheepishly I have to admit I found this line about 3/4r's of the way through.
snapshot.disabled = "TRUE"
That'll be the reason then
Doh! Given that you and I disabled snapshot capability differently this will be the place to check for the possible ways to end-up with disabled snapshots.