When I use these commands : vmkfstools -i vmfs/volumes/mydatastore/myvirtualmachinefoldername/my.vmdk vmfs/volumes/mydatastore/newmachinefoldername/new.vmdk -d thin
Unless your working directory from where you execute this command is /, you would need a "/" in front of the paths.... so try:
"vmkfstools -i /vmfs/volumes/mydatastore/myvirtualmachinefoldername/my.vmdk /vmfs/volumes/mydatastore/newmachinefoldername/new.vmdk -d thin"
/Rubeck