Can't try that tonight but I will tomorrow. I'm starting to wonder if its my IR's. I use my own exclusively that I shot from my rack tube amp and cab setup. I might need to try some stock cabs and see if that's it.
I believe you said you are using Herbie CH3. That model changed. If you want the sound of 1.03 do the following:
Increase Input Trim to 2.0
Set Low Cut Freq to 160
Set Preamp Bias to -0.1
Set Tonestack Type to "GERMAN V4"
Set CF Time to 3.12 ms
Set CF Ratio to 0.183
It's probably the change in gain that you are noticing most. Since the amp doesn't have a bright cap you can also just turn up the Input Drive instead of increasing Input Trim.
Note that the updated model is more accurate as we redid the model because the Tonestack changed.