Are you able to install this software manually on these 64 bit systems? When we run packages remotely from the core, we run the with no interaction as its all hidden in the background. Its possible some erroneous prompt is coming up on the 64 bit install that is waiting for a user response but due to the nature of how its run, that prompt never shows up visibly.
I would attempt to run the package manually in the same method that you're having IEM run it and observe the behavior with interactivity present.
We can install it manually on 64 bit systems with no issues. I was finally able to distribute successfully though our portal manager by removing the MSI that was wrapped in the EXE. I created a package for the MSI, and removed the exe package and it works great on either 64 or 32 bit operating systems.