These VM's have 2 disks but on different datastores.The name of the disks is the same, so both disks are named VMNAME.vmdk but one with capitals, other without capitals. The disks are on different datastores.Error: The specified item was already backed up or backup was not completed. Failed to download disk. End of file Failed to upload disk. Agent failed to process method {DataTransfer.SyncDisk}.
In v7 there was no problem with the back-up of these VM's and their disks. Support have confirmed this is a bug in v8. The soonest they can fix it is with Patch 1, due for at least another month.
A possible workaround is using storage vmotion on 1 of the disks, and the assumption this will change the name of the disk. However I tried this, and the name did not change (vsphere 5.1). Another option is manually (with powercli) changing the disk name, but for this the VM needs to be powerd down which is not always easy to do on production VM's that run 7 days a week.