Well, as would be expected, they are very close. The i1Pro 2 technically has a slightly larger gamut. This larger gamut is mostly seen in the the shadows, red, cyan and especially yellow highlights. The ColorMunki is slightly larger in the saturated blues. The attached gamut plot shows the i1Pro 2 gamut in the white, see-through wireframe, so you can get an idea of both gamuts at once. Where you see the wireframe, the i1Pro 2 is larger. Where you can't see the wireframe is where the ColorMunki underneath is poking through. Like I said there's not a big difference. It's not surprising that you would not see a difference in the printed output.
ColorMunki: 473,000 cubic Lab
i1Pro 2: 487,000 cubic Lab
I then switched the ColorMunki to wireframe and zoomed in on the shadow areas. There's a divot in the bottom of the gamut. An outer boundary point suddenly shoots up inside the gamut skin like a little pocket. What this means is that any color that you want to print in this pocket area (dark orange or brown) won't be printed correctly but will be lighter than it should. My guess is that when you were measuring with the ColorMunki some light sneaked around when you were going over a shadow patch and it measured too light? (These are usually caused by measurement errors.) Again, it's a relatively small error, and you might not notice, depending on what you're printing. The i1Pro 2 gamut showed no problems like this; everything looked smooth.
I guess I should point out that these gamuts (above) are showing you the total gamut of what the printer is capable of printing, which is different from the rendered gamut. Below is the rendered gamut, what the profile will do when sending your colors to the printer. This might be the gamut shape that you're more used to with i1Profiler (though not in such detail). The rendered gamut is pretty much the same. Some blue / magenta is stronger with the ColorMunki, and yellows are stronger with the i1Pro.