How big of a clay pot base did you use? Got a link?
I planned to put a probe somewhere in the middle of the top grate. I just received an ET-73 today but, I used an oven thermometer on the grate over the weekend, just to double check against the lid therm. I did notice that sometimes they were dead on with each other, and other times they were around 30 to 50 degrees off from one another. Unfortunately, I don't remember where the oven therm was located in relation to temp differences between the two. I kept moving the oven therm.
I smoked a few hot dogs while doing a rack of pork spares this past weekend (twice actually, once Saturday, and once Monday) and I noticed that the end ribs cooked much faster than the middle section. (I have the 18.5 WSM, so a rack of spares barely fits on the grate.) Sounds logical to me. Why wouldn't the ends cook faster? However, I noticed that a couple hot dogs got really cooked while the other couple didn't really do much in an hour. I noticed the well done dogs were right on the edge of the grate.
It occurred to me that most of the heat from the fire comes right up the sides, around the water bowl (I said "DUH" to myself). So, anything on the grate that is hanging beyond the edge of the water bowl is gonna cook fast....or show a higher reading if it's a probe.
This seems to agree with what you were told about your probe possibly being too close to the side.
I'm also curious to see where others mount their grate probes.