You didn't mention if this is a popper/coretto?
Just my thoughts - if you are roasting in a closed environment I wouldnt expect to see a temp change. From my limited experience I don't recall crack temps changing.. Except when making changes to the probe. I find that you will ramp faster when it's warmer but as you said heat can be dialed back
If it is an open environment then it would hazard a guess that your observation is indicative of the inaccuracy (note not inconsistency) of your current probe placement. In this case I don't think it is necessary to try to manipulate anything to get the temp back to the initial probe temp
Maybe the observation here that needs to be made is are you hitting first crack/second crack at around the same time as previously? I think this will be more significant than the temp first crack/second crack starts.
As a general thing you are going to be able to burn off acids quickest starting on the lead up to second crack (when it starts smoking heavily), so as you said lengthening the roast should help you mute the acidity.
Anyway hope it help =)