It shouldn’t matter so much. Personally I measure right on top. However, it probably is best to stir well before measuring to ensure the most representative sample. Also, be aware that temperature has a very significant effect. If measured warm at mash temperatures around 150 F, the reading will be 0.25 lower than it will be at room temperature. Room temperature is the standard. pH should be about 5.4-5.5 at room temp. If measuring directly in the mash tun (as I do), expect 5.15-5.25.
I have to wonder if you were experiencing a temperature effect.
