I have an OCD thing that requires me to always purchase "2" of the same amps (and preamps), so I can compare them with different tubes as well as different settings to see what sounds better to me.
I don't believe those two JP-2C amps would have had the same tubes in them since Mesa Boogie has used different tubes over the years (preamp and power tubes) due to tube shortages/stock/availability (something that has changed/affected the tone of the amps for good/bad and personally annoyed the hell out of me).
Do you remember if the tubes were the same exact tubes?
I have two JP-2C's and I did find they sounded different initially until I had swapped out the tubes that were different.
Now they sound more like the same amp once the tubes are/were the same in each amp.
The JP-2C is a great amp with either transformer, however, the sound can be affected (slightly or a lot) by the tubes, the guitar, the pick-ups, the cab, the pick, ......
Fortunately, these are the cheaper things to change up for tonal differences and even the feel of the amp.
I always tell friends to explore using other things to get their ideal tone like the tubes, the guitar, the pick-ups, the cab, the pick, ...... before getting rid of the amp if they had heard the amp somewhere (local-show, concert, YouTube, .....) where they had initially felt the amp sounded great to them.
Unfortunately, the ideal tone for each of us can be a very subjective thing
However, this version or the latest one will still give a person some GREAT amp tones and playing experiences!!