The error message would definetly help. Let me know how your LiquidWare Labs Profile Unity testing goes. We are a 4.6 View shop testing Persistent disk with linked clones as well as Floating VMs.(what you call NPLC).
I would like to know if Profile Unity will not only carry over your window settings, but your manual(Apps installed outside of ThinApps) apps as well.
Have you tested any other profile type of product that would be beneficial in a Persistent Disk - Linked Clone environment???
We managed to get past this issue. Turns out it was AppV that was the cause. Disabling the service before taking the snapshot, setting it as 'disabled' until the VM was almost 100% ready (final reboot turned it back on) fixed the issue.
So, if anyone out there is having issues with non-persistent linked clones deploying, and has AppV on the master image, try disabling the service while deploying.