2004 34" Alp[ine coach jake brake

Has anyone out their have any information about the problem that W-R/V is having with the low jake when the RPM gets down to around 1050 RPM it picks up a growl and the DB increases as the RPM drops until it get down to around 900 RPM and then torque its self out and then it free wheel as if you had your foot on the brake and then take your foot off of the brake and then you free wheel.
I am having this problem with the 2004 Alpine that we have.
The Alpine people says that the Cummins and the Allison people say that this is normal with the 400isl Cummins and the md-3000-mh Allison and that it is a torsional thing and that it does not hurt the transmission or the engine. I disagree with their findings and can prove it.
Another person has a coach just like mind and had the same problem and a Allison & Cummins shop in Calf. found that the ecu for the Cummins was program for a exhaust brake and the Allison was program for a retarer. So they reprogram the engine ecu for a jake and the transmission pcm a jake and enable the J-1939 and now they work fine.
What I don't understand is that the high jake work fine before they reprogram the ecu and the pcm. Does the ecu and the pcm have two setting on them? Why was the high working at all if the ecu was set for a exhaust and pcm was set for a retarer. And what part does the J-1939 play in this?