It turned out to be the apparently not-so-equivilant transistor I had used.
When building up the NG2 I just moved over the 2N3904 I had used in my M&M build, and had similar results. The old Futaba FG worked but the newer 6EXA didn't. The 2N3904 was listed as being a cross for the BC550C.
So then I went with a BC107 as listed on Alessio's schematic (which I had) and it worked for both builds! I then also tried a 2N2222 and it worked just fine too.
Back to the scope. As I mentioned previously the amplitude of the signals at the base of the transistor were the same. But, at the collector/pin 21 of the pic there is a difference. With the BC107 it is 4.9v with both transmitters on both builds. With the 2N3904 it is 4.2v (FG) and 2.8v (6EXA) on the M&M build. On the NG2 it is 3.8v (FG) and 1.7v (6EXA).
I looked at the data sheets for these transistors but I don't know enough to tell what might cause the difference.
At least it made me get out and play around with the scope again. It's been fun building these up, and I might even use them with a simulator now!