AeroPod, PowerPod and Newton

I just got my Gen III iAero. I have two basic setups: one of me alone and one of me towing my daughter in a trailer. I had two profiles for the Gen II and I just did the calibrations for both with the Gen III. My problem is that the Gen III measures significantly lower Aero and Fric numbers. I will repeat my cals tomorrow and will upload that stuff if it has the same behavior but before I go to the trouble of uploading stuff I had some general questions:
If I'm changing NOTHING except for the head unit, should I expect the numbers to be nearly the same? They are inherent to the bike's characteristics, not the unit, correct?

Also, I have the same problem others have posted about with the unit getting stuck in the setup mode and needing the battery removed to restore function...does that bug, whatever it is, have an impact on the ride data or cal data that is in the unit at the time?

Please send ride files from your Gen III. If possible also send comparable ride files from your Gen II. Send them to jhamann@velocomp.com

False alarm. As it turns out it didn't get the right value from the cal ride the first time.
The new numbers make a lot more sense:
The Aero value from the Gen II was .338 and the wind scaling was .988 (Cda of .343)
The Aero value from the Gen III was .202 and the wind scaling was .553 (Cda of .365)

The first time around with the Gen III the wind scaling was 1 which means (I assume) that it wasn't recovered from the cal ride. I didn't think much of it because my wind scaling on the Gen II was pretty close to 1 so for both profiles the Aero pretty much equaled the Cda. That was my mistake.

Even though they have the correct Cda values now I'm a little surprised that the Aero values are so different. Is it normal to have such drastically different wind scaling factors for the same setup? My unit is stem mounted and I literally didn't change anything other than the head unit.
I figured if other people have similar problems it might be worth answering here. If it's not normal I'll send the files in.