2019 Tacoma - stuck in 4th gear

A few years back I had the Magnusson Supercharger installed. It has run beautifully since that install and tune. The Tacoma Shifting (searching) issue was partially resolved with he added power, but not all if it. I recently installed Nitro 4.88 gears and now have an error/problem and all input so far seems to be a computer/program issue. Issue is - after 30+ mins of highway driving, when downshifting in traffic or to pass, it will stay in 4th or 5th gear. The only way to clear the error is to pull off the road for a few mins with the engine off. Shifts normally for a while and then will repeat. Has not seemed to be a difference in outside temp and no overheating issues exist. I did swap all fluids (trans and both diff?s) to see if it was mechanical. Any chance you have seen this? Any known work around?

Anyone out there that can do or recommend someone to redo the tune program on a Magnusson Tacoma?