Microsoft Intune or Endpoint Manager is awesome but also a pain if something does not work as expected. For example, if you create a package that simply imports a reg file, it will import the keys under SOFTWARE\WOW6432Node (WOW or SysWoW means Windows32OnWindows64). This is normal behaviour because Microsoft Intune Extension runs as a 32 Bit process on Windows. Therefore it does not know about the 64 Bit architecture.

So the solution is to run the reg command with this option. This will import the keys directly under SOFTWARE\…

reg import file.reg /reg:64

There are other approaches to this but my solution works and is the fastest in my opinion.