Kris,
Your results are definitely puzzling, but that doesn't help you at all. You already know that.
I am certainly not an expert with these smokers. I'm still learning and have gotten a whole lot (more than I probably deserve) of help from the folks on this forum, so I would encourage you to hang in there because eventually you will get this worked out. I have had my #2 with separate Auber controller for about 2 years now. I installed the box temp probe permanently and modified the wiring to bypass the internal controls on the old-style #2, so I essentially have the same set-up as you. I have learned that once you run the autotune with the dummy meat load (I use a half-size pan with sand dampened with ice cold water), the smoker will behave rather wonky when there is not either meat or a similar dummy load in it.
As far as the temp probes are concerned, have you tested them to insure that they are reading and responding correctly? I do this by mixing a batch of water and ice cubes. Keep adding ice until it doesn't melt anymore. Your liquid should be at about 32 deg F. Put each of your portable probes (including the Auber meat probe) in to see what they read. Label the probes and record what they read for future reference. On my #2, the way that the internal temperature probe is installed, I can pour this ice cold mixture into an insulated coffee cup and tilt the smoker forward and place the probe through the sipping hole in the lid of the cup to get the probe into the water. You can read the temp on the Auber controller. (I'm not sure how the temp probe is installed in the 2D, so this may or may not work, so you may have to be a little creative.) I do the same with boiling water. Test the portable probes and make sure they read 212 deg F. Pour some water into the coffee cup and test the probe in the smoker. (It probably won't be quite 212 deg, but you can use one of your portable probes to see what it should be reading and compare.)
Once you know that all your probes are accurate, on your next smoke (like a butt or brisket) put several of your portable temp probes in the meat along with the smoker (Auber) meat probe and compare the results throughout the smoke. That should tell you if your probe is placed correctly or not, but since you are not new to smoking, I would assume that you have plenty of experience on where to place the probe in all types of meat.
I cook a lot of pork butts. (Many of my friends keep bringing me 2 and ask me to smoke both and keep one. Free food is good!) I noticed last weekend (when I ran the test on the wood chunks that I posted elsewhere) that my smoker took about an hour to get up to 215 deg (the temp I had my Auber set for). Once it got to 215, it stayed there (within 1-2 degrees) for the entire smoke.
When I first got my smoker, I had problems with the infamous "belch" so I got accustomed to ramping up the temperature. This is a whole other discussion that I don't want to get into in this post, except to ask have you noticed the "belch" at about 15-30 minutes into the smoke? You may want to try on your next smoke setting the controller to around 140 deg for the first 0.4 hours and then up it to your final smoking temp to see if that makes any difference.
I hope that some of this helps. Keep us posted on your progress.