So I'm sure you made sure the tranny is topped off. I remember reading LMS said something about adding more then it needs if it's acting up after the tune is installed.
Different note, I added no shudder to mine when it wasn't acting right and it helped a bunch.
Plus I don't know if these tranny programs are related. But I read on my Jeep forum that the Cherokee and Ford used the same programmer for some auto tranny applications. And the Cherokee Trailhawk will ( with 6 speed auto or could be

never even shift past 6 unless you make it.
But i hope you get her sorted to your satisfaction.
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