[Accelo]

Someone will correct me if I'm wrong but I think the only thing the improper ratio setting would effect would be the speedometer.

An incorrect speedometer reading isn't the only issue. Shift timing is also affected.
The computer reads, speed, throttle or engine load and engine and transmission temperatures to schedule shift quality and timing. If it is cold out the transmission shifts late till it warms up.
Tuners can change the speedometer reading which affects the transmission. They can also set WOT shift rpm and this can be different for each gear. The computer also anticipates shifts and raises the transmission's line pressure before the shift and then reduces after the shift. Not even touching on "torque management" which will reduce engine power for the shift.
Kind of crazy isn't it?

My truck ran night and day different after the tune. I hated to do it as I considered it overpriced. Afterwards, I thought I received every penny worth as the truck ran so much better.
I drove it home, from the tuners, on the back roads and embarrassed myself in front of the cows.... It was a blast.

You didn't mention if your tune was on a dyno or if your motor has an aftermarket camshaft.
I had a small exhaust leak 6 inches below the O2 sensor and the tuner knew and even could tell me what side it was on.
The details the OEM's go through to get this correct is astounding. The smallest item like an exhaust or vacuum leak upsets the system.
Do you have an exhaust leak any where slightly down stream or anywhere upstream from the O2 sensor. That will wreck havoc with how your motor runs.
Cheers