Forgot to mention, you can also find more scripts/resources located at:

http://engineering.ucsb.edu/~duonglt/vmware/

What issues are you having? Once you've created your pristine image and generated the Linked Clones off of that base image, you can use the following documentation for further configurations to make each LC unique: http://communities.vmware.com/docs/DOC-9201 , this is the implementation that my colleague Tuan and I have deployed into production at UCSB.

=========================================================================
--William
VMware ESX/ESXi scripts and resources at: http://engineering.ucsb.edu/~duonglt/vmware/

Are you creating the new snapshots using the VI Client or through the console? What version of ESXi are you running? In either case, we've not heard or run into this issue before, if I get some time will try to test but I'll be pretty busy with some new projects.

=========================================================================
--William
VMware ESX/ESXi scripts and resources at: http://engineering.ucsb.edu/~duonglt/vmware/

I had the same problem and it turned out that the clone was in a template mode.
http://hash-depot.blogspot.com/2009/05/vmwares-esxi-snapshot-removal-problem.html
Check advanced settings for templateVM and if its set to "true" change it to "false". Worked for me.

just changed the script a bit, thought i might share back

vmdks_count=`grep ^scsi "${GOLDEN_VM}" | grep fileName | awk -F "\"" '{print $2}' | wc -l`
vmdks=`grep ^scsi "${GOLDEN_VM}" | grep fileName | awk -F "\"" '{print $2}'`

what changed : I changed the grep scsi to ^scsi
why : I had a floppy mounted vmscsi*.flp that contains the drivers to install xp. This blocked me from doing linked clones even after i detached the floppy, because it was still in the config. Grepping on ^scsi makes more sense because this is the pattern you are looking for

macfile() {
#grab mac addresses of newly created VMs (file to populate dhcp static config)
if -f ${LC_CREATED_VMS} ; then
for i in `cat ${LC_CREATED_VMS}`;
do
TMP_LIST=${LC_EXECUTION_DIR}/vm_list.$$
VM_P=`echo ${i##*/}`
VM_NAME=`echo ${VM_P%.vmx*}`
VM_MAC=`grep ethernet0.generatedAddress "${i}" | awk '{print $3}' | sed 's/\"//g' | head -1 | sed 's/://g'`
while
do
sleep 1
VM_MAC=`grep ethernet0.generatedAddress "${i}" | awk '{print $3}' | sed 's/\"//g' | head -1 | sed 's/://g'`
echo $(grep ethernet $i)
done
echo "${VM_NAME} ${VM_MAC}" >> ${TMP_LIST}
done
LCS_OUTPUT="lcs_created_on-`date +%F-%H%M%S`"
echo -e "Linked clones VM MAC addresses stored at:"
cat ${TMP_LIST} | sed 's/[:digit:]/ &/1' | sort -k2n | sed 's/ //1' > "${LCS_OUTPUT}"
echo -e "\t${LCS_OUTPUT}"
fi
}
#mac generation is done after the vm powers up. if you want to generate this file you will need to power on the vms first
#macfile()

what changed : Made a function to generate the file with static macs
why : Here in my version the mac addresses where only generated after the machine was powered on. This meant that the script kept looking and waiting for the mac address to be written to the vmx file. Since I don't need these mac addresses i just disabled it.

Hope it helps