I dont see any branching in the snapshot manager. Looks like the chain is broken or handled incorrectly.
Please take a backup copy of Ubuntu12.04LTS.vmwarevm before modifying any files within it.
Try this :
Edit the vmx config file and change the hard disk to Virtual Disk-000005.vmdk .
Edit Ubuntu12.04LTS.vmx file in textedit
Replace
scsi0:0.fileName = "Virtual Disk.vmdk"
with
scsi0:0.fileName = "Virtual Disk-000005.vmdk"
For details on editing vmx refer
VMware KB: Editing the .vmx file for your VMware Fusion virtual machine
Running the Virtual machine from base disk should have worked though.