Hey Chris,
I've had the Mackies for about a year....they do seem to be tricky to learn the low end on.
Could some of your problems be room related?
A few things that helped out my low end(or at least seem to make it more accurate) were getting the Mackies off my DAW desk and onto some heavy speaker "stands"(read Cinder block
) and usind a set of Auralex Mo pads under the Mackies
.
Hope that helps