Hmm. So the only crossover you've got is on the sub itself. What do you currently have that set for? It's harder to blend speakers with sub when that's all you've got; the bass from the speakers has to match the sub pretty well, and the sub has to be pretty fast, otherwise you get a bit muddy. I'd probably set it around 50 or 40 Hz, given the option. Also, does the sub have a phase control and have you played with that?
I agree about using the high level inputs on the sub; mine did not play nicely with that, although it didn't completely fail as yours sounds like it did.
I also experienced the joy of adjusting the volume on the sub/cd, although since you've got it on pre-outs, it won't be so bad for you.
In your testing, it sounds like you were trying to listen to the sub by itself, without the M60s. That's going to sound pretty odd; I'd test with the sub and 60s together and try to match it up that way.
What source material are you testing with? I thought I saw something about pipe organ. While that is undoubtedly a good sub workout, the bass is not necessarily repetitive. I tend to like using Sting--Mercury Falling or Brand New Day to test it out. Those particular albums have bass that you simply won't get through the M60s (I don't get all of it through the M80s, and certainly not nearly all of it through the M50s!), and it's pretty repetitive and constant if you pick the right track. Of course, it may also drive you insane depending on your musical preferences.
