I believe I found the issue which was caused by an entry called Isuser which is an environment variable used by InstallShield.
It was leftover on the machines that had this issue, and if I deleted the variable before running the registry cleaner the problem went away.
I looked around and several of my machines had this variable which I quickly remove, however some of my computers did not have such an entry.
I would recommend removing the variable by going to system, advanced system settings, environment variables, and looking at the top box.
If the cleaner removes that users environment entries while it still exists, the desktop gets whacked as the user is deemed missing.
That causes the loading of the desktop to simply stall, which happens very early in the process and the results are not good!