Good to hear it's sorted now.
For anyone who encounters this in the future, here's what I think was going on.
I was taught that reversing the conductors of the extension/compensating cable results in an error of twice the difference between the temperature at the cold junction sensor (in the controller) and the thermocouple terminal block (presumably on the outside of your oven).
If you are using thermocouple extension cable for the wiring, it will be exactly the same material as the thermocouple legs themselves. Each junction of the dissimilar metals becomes a thermocouple (compensating cable will give a similar effect, but over a narrower temperature range).
I've seen it a few times myself, but usually the connection is far enough from the hot zone to be at about room temperature (we design things that way to allow the use of cheaper compensating cable with cheaper plastic insulation), so the errors are not that big.
Section 5.7 of the Auber manual shows a connection diagram for differential temperature using two thermocouples connected series, but in opposite polarity. I think your original connection was something like that, though probably with 3 "thermocouples", with each of the introduced junctions having the opposite polarity to the measuring junction.
I use a different thermocouple arrangement to most, so I don't know what sort of connector temperature is normal, but I have measured a surface temperature of 112 degC/233 degF on the outside of the soft firebrick of one of my homebuilt HT ovens.
I'd normally expect the thermocouple to provide an easier heatpath than the soft firebrick, making the connector block hotter than this, but there are lots of other variables and these will depend on some of the finer details of your design. Taking that value, and assuming the controller is at around 20 degC/70 degF, we are looking at a difference between the two of around 160 degF. Multiply it by two, because there are 2 introduced junctions, and you get an error of 320 degF.
It sounds like your error was probably bigger than this, with the most likely reason being a hotter connection block.
Regards
Tim