Ok so not the trans. I’d say (guess) that your jake isnt cutting out early enough. For example, if its supposed to automatically cut out at 1000 rpm (typical), but it isn’t happening until 800, it would start to stall the engine. Since it may also have a speed based cut-off, with a speed sensor turning off the jake at around 15mph, that could be suspect too, but I think this is less likely.
You can check this by watching the tach as the issue occurs. This could be electronic (ECM adjustment) or more likely mechanical (Jake system service). There is a maintenance schedule but it starts at 100k miles, so yours has probably never been touched. But like so many other things, these maintenance schedules are intended for high milage vehicles based on use, not time, so the schedule may not be sufficient.
Either way a quick visit to a Cummins or Freightliner shop will likely fix it. My guess is you are manually compensating for whatever the issue is by shutting off the Jake when it should go off automatically.