Well I use AP racks however I never knew there was a difference in heat between side and flat area.
I have some AP racks with a slot for the probe so I assume yours is not one of those models?
I also have some with no groove (economy hatchling racks) and I just tape the probe in between some tubs.
Any chance you can move the probe closer to the tub?
Either way what matter is the temp in the tubs and therefore you should adjust your t-stat based on that.
As for an explanation on why the difference I guess I will have to check mine and see the difference if any.
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