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try to clone to flat with vmkfstools -i
http://kb.vmware.com/kb/1028042
vmkfstools -i "/vmfs/volumes/path/example/example.vmdk" "/vmfs/volumes/path/example2.vmdk" -d thin
# the vm must be powered off
and then clone via vcd or vc
New-CIVApp -Name vapp_name -OrgVdc org_vdc_name -VAppTemplate Template_name
if the vcd has problem then you can do it via vc if vc has problem that you much clone the the disk (flat) shile the vm is powered off and create new vm and then attach the disk that you cloned with vmkfstools.