i'm also on the same version and found the NEO 2T to be reading ~ 15-20 Watts Lower than my Stages Power Meter. Since i've always worked with my Stages, i'm using that for Power. I found the NEO 2T to fluctuate more, even with Powersmoothing turned on when i work out. I Sure hope they can come out with another firmware to address this.
I found the NEO 2T to fluctuate more, even with Powersmoothing turned on when i work out.
Sounds like you are depending on instantaneous power, which given the higher sampling rates of the Tacx Neo 2T should yield much more fluctuations in the measurement of instantaneous power. Might I suggest using 3-second or 10-second avg power metrics for training instead? Personally, I am going to put more faith in the accuracy of the Neo given Tacx's manufacturing and calibration processes in the factory in the Netherlands versus the Stages production processes.
You have tested your NEO via Tacx Utility though right? And works ok? Can you ERG with other App? If your answer is Yes to all my questions, sounds like a settings in TR.
ALWAYS trust the higher number! 
I only did this test once (since I usually use a regular set of pedals on my indoor bike), so maybe I screwed it up...