Gerald,
The gear selection that the Allison will use when the Jake is engaged is in the Allison ECU program menu. I'm not sure if that is the only Allison program option regarding the Jake/Exhaust brake that is available.
I think I had read one time that there was a programmable offset value, in MPH, so that if the Jake was programmed to come on when the throttle was fully off while using cruise control, that the throttle and cruise control would not be immediatly be reactivated by a loss in speed by the Jake. Something like a 2 or 3mph window so the systems were not working against each other. I would guess that option, if available, would reside in the Caterpillar ECM program. This could also have been a Cummins or a Detroit Diesel post that I might have read discussing this, it has been awhile....
As an aside I have had some travel experience, about 1500 miles now, with the Allison reprogrammed to make all gears available using the Jake Brake. I am a fan of this option so far. I find for interstate travel on most grades in the east through PA, WV, VA, TN, AL, 6th gear using a toggling from 3 to 6 cylinder or sometimes just the 6 cylinder position holds your speed or it will slow you down at a slow rate of speed change. I think this option saves fuel by having the Jake not down shift and brake more than is needed. You could toggle the jake on and off in a lower gear but that could also encorage more shifting in the sequence and it seems like more wear and tear than is needed. I think once or twice I manually downshifted to 5th on this trip. I certainly found this 6th gear option to be a stress free driving experience when compared to the 4th gear being forced and the over revving issue......glad that is behind me. In the west I would expect that 5th and 4th gear would be invoked more often but my guess is that having 6th gear would be used a lot on interstate grades that are not excessive there also. My net is 6th gear use with the Jake is very useful.
I think what I will do is get some transfer numbers and put a 5 and a 4 on the speedometer where the 2100RPM point is in those gears to guide me. I'm still not sure if I invoked 5th or 4th manually, if the Allison understands where the C12- 2100RPM point is and therefor would protect the engine by not downshifting to that lower gear while the Jake is engaged. At least before, Jake braking had priority over RPM, and I do not see any programming change that was made in this process that would have eliminated that issue. Still a little foggy on how that one would work now and I did not want to test it...
Later Ed