I just had to get a new pcm and had it flashed with the factory tune, now I cannot reflash my custom tune. What do I need to do?

Here is a log in 2nd gear manual wot all the way to rev limiter. The plugs are brand new and checked for spec.
The builder is a reputable jeep stroker builder here in NC that says it should go to 6000k no problem.

Any update on this?

Here is my tune. I have the manual params set to 6000 for both neutral and in gear although it is a manual. I'm not sure if the tuner also set the rev limiter.
I also have the most recent log. btw I have 37" tires and the stock 4.11 gears.

I have a 2006 jeep rubicon stroker... For some reason the rev limiter increase does not work. Is this a known issue? I have a custom tune and the tuner set it to 6000 but the engine still hits the limiter at the factory spec around 4900.

Also the tire size changes dont work with the rubicon ...