I said this almost a year ago. EVERYONE (except Jonathan from Tone Junkie, who heard the same thing) was desperately calling me everything from a liar to deaf. However it was clear to me within seconds of playing.
I even posted a waveform from a test with a looper pedal in front of a mk 1 and a mk 2 unit. It’s not as much the “eq” of the sound that is different, though it is ever so slightly different. But the dynamic response is noticably different, in that profiles with edge of breakup, has the breakup point feeling different.
Jonathan is one of the top commercial profile sellers. Firstly i trust my own ears/ findings, but i also trust his ears. But then G String popped up in the thread telling everyone that i was wrong and they sound exactly the same, and ofcourse this added a bit of fuel to the stake i was being burned upon. 
But i don’t care. My mk 1 rack does NOT sound exactly the same as my mk 2 rack, nor does it have the same exact response. Note that this is MORE pronounced with single coil pickups. On humbuckers there was really no noticable difference.
Is this a problem for me? No, actually it is a non issue, after a couple of gigs i had adjusted to the slightly different feel, and since i was met with “you are wrong” i chose not to contact support.
How does the difference feel? It’s explained best this way, (and all of you with home or commercial studios will have experienced this). It felt just like when you go from one brand of audiointerface to another with different AD and DA converters. Your sessions sound slightly different in your studio monitors and you have to adjust for a couple of weeks.
And this is actually what i put it down to, and i said it already then; sounds to me as the converters are different in the two units, after all there is approx 10 years between them, so to me it would make sense if the hardware had changed over the years.
I don’t even know why i bring it up here again, since last time was just……not nice….. but hey, i’m probably wrong deaf or lying or whatever you can call me….
Post script: The mk 2 unit brought one HUGE improvement. The midibuffer is better. No longer would i experience errors in wrong loading of rigs when going from one performance to another when snding a midi pc at the same as a midi cc. For that alone the mk 2 purchase was worth it, because this was driving me insane.