@Joe-Schmitt, I encountered the same issue after recently upgrading from FOG Server 0.32 and the old FOG Client to 1.4.4 and 0.11.12, respectively. Deploying the same snapin that previously modified the AutoAdminLogon key on Windows 7 64, no longer seemed to affect the registry (still deploying to the same OS).

After some testing, I found that Windows File System redirection was the culprit. FOGService runs the snapin with the 32-bit executable (cmd.exe, cscript.exe, reg.exe, etc.) because Windows redirects %windir%\system32 to %windir%\SysWOW64. This caused my registry update to modify

HKLM\Software\Wow6432Node\Microsoft\Windows NT\CurrentVersion\Winlogon

instead of

HKLM\Software\Microsoft\Windows NT\CurrentVersion\Winlogon

Don’t know why my old FOG ecosystem was unaffected, but here are some workarounds I’m exploring on the snapin side (links document the ideas—YMMV):

Prefix the command with %windir%\sysnative (only works on Windows 64 bit in a 32-bit shell), which can be done in directly in Snapin Run With or coded into the script
File System Redirector mentions using %windir%\sysnative

Create a symbolic link to call a 64-bit version of the executable
Open 64bit command prompt in 32 bit command prompt

Force REG.exe to write to 64-bit registry location with /reg:64
https://ss64.com/nt/reg.html

Example VB Script that sets Autologin - untested