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I found the solution.
When adding packages to our repository there is an "As Admin" option. If that is selected and credentials are incorrect or not set then the install scripts fails/stops when trying to open an elevated session on the target PC. I re-added packages without selecting "As Admin" and now they're auto-installing.

Correct,

The As Admin setting expects that you have all the credentials setup for the client in the client configs so that when the LTscript pulls the "admin" user/pass there is something there for it to use that will work on agent.

Otherwise when not checking that box it will use the default user the agent runs as which in most cases is SYSTEM which has all rights needed.