Corrections due to torque limiters won't log under the timing correction parameters though, will they? As far as I know only correction due to knock does.
My car is manual, but it showed the same sort of corrections post shift, and only on pump gas. Recently though, I realized that the bin I used to make my map originally came from an automatic car, and there were a large number of differences between my car's stock bin and my custom one that didn't correspond to any of the currently defined tables. I copied over all my defined table changes into the stock bin, flashed it, and now the corrections are completely gone. So, for what it's worth, there may already be an undefined flag/table that modifies timing reintroduction speed/whatever is causing this issue.