I am not familiar with the keyboard setup for this new Orbiter Keyboard, but I am betting that the remapped keyboard.cfg keys do not take into account the custom keyboard commands for the DGIV's flight computers. That is custom to Dan's Module for the DGIV. IMHO, I don't think there is a quick fix for this outside of using a standard keyboard with the typical key layout. Hence, the reason why the author asks you to save a copy of your original keyboard.cfg file. One other option would be to do a stare and compare of the new config to a list of keyboard commands to the DGIV's and reassign keys in the keyboard.cfg that conflict with Dan's custom keys.
Keys you expecially want to avoid are P, S, C, and E (Pro, Spec, Cancel, and Execute)
I hope you found this helpful.