Any update on this issue. I am having the same exact problem with a 2001 7.3 F250. AE will connect to and read DTCs from the Enhanced Powertrain module with no problems, but when retrieving DTCs from all other vehicle systems, (i.e. Anti-Lock Brakes, Airbag, Park Aid, GEM/Central Timer, Overhead / Trip Computer) it shows "No response from module." When trying to connect with AE to any of the systems showing "No response from module", it says "Could not establish communications with the controller..." ABS light is on and I am trying to pull ABS codes. No other problems with the vehicle, everything works as it should, as far as I know.
Also, I tried the same exact thing with AE on a 2002 7.3 F250 and everything works as it should, all systems connect properly, load and display all sensors, and shows all DTCs on every system / module.