My 1997 CC Allure has a PRXB Pacbrake, exhaust brake which replace the original sometime around 2005. The coach now has 67000 miles on it of which I have put about the last 36,000 on it. The engine ...
Transmission problems on an Allison 3000 transmission are very rare.
If no exhaust leaks (i.e. no sign of black soot as discussed above), my next step would be to contact PacBrake and get the back pressure specs for your brake. Then temporarily install a gauge on a 6'+ hose connected to the pressure port on the PRXB, route the hose through a bedroom window or up through the bed and verify actual back pressures while driving.