Hi AkashH,
Thank you for your reply.
I have tried clonning the VM but. After I run the diskpart utility is OK. However, after a restart of the VM they are again all over the place. I have tried clonning it but since the drive letters are messed up it just replicates the issue.
A co-worker suggested that it might be Storage DRS. He thinks that by moving files (vmdk) around somehow SDRS scewes up the partition table. I said it is complete rubbish, SDRS has nothing to do with it. Anyway. I shall wait to see if someone else has come across this issue.
Regards,