I created an MST for Acrobat DC Standard (volume license) using the Customization Wizard. I then installed Acrobat using setup.exe and upon first run, I noticed that only the computer-level customizations were applied. For example, the PDF Printer settings I specified were there, and a file that I specified to be copied to the Program Files directory was there. However, none of the HKCU registry settings were applied. Another setting that was ignored were the shortcuts that I specified to be included in the Tools Pane.
I understand that the custom HKCU settings are stored in: HKLM\SOFTWARE\Adobe\Adobe Acrobat\2015\Installer\Migrate, and they are supposed to get copied to HKCU on first run. I've read that there is a bug with Reader DC that places these settings in the wrong location, but in my case with Acrobat Standard, I checked and all my customized registry settings are in the correct place in HKLM. They are just not getting copied to HKCU on first run. Any ideas?