The upgrade process differs between a traditional .x upgrade, and the Addon install process used for PulsePAK, etc...

To clarify - PAK uses the baked-in install.bat file located in the: "GE_MDS\PulseNET\addon-install\bin", and does not have an accompanying "install.bat" in the .zip itself.

Upgrades or Hotfixes such as the 5.0.1 will come included with a 'bin' directory and subsequent install.bat. This should be used instead of baked-in addon install option for a traditional dot number release.

In short - Upgrades/Hotfixes come with own new install.bat - addons such as PAK use existing GE_MDS folder structure.