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Incompatible pedals?

For the longest time, the only effect I had was my Bass Big Muff Pi. Finding it a bit lacking, I picked up a few more things. Rusty Box and a Mini for more dirt variation. Rusty box is always on. I have a jazz bass and a jaguar p/j setup. When I run the mini into the muff with my bridge pickup on either bass, its all good, except it loses a little oomph as to be expected. However, when I run the neck pickup, it gets all squashed and farty. The muff alone is fine, and the mini alone is fine, but together its no good. Has this happened to anyone else? Is it just the crappy muff or is this a common occurrence when stacking dirt? I don't have much experience with effects beyond these, so I'm not sure what the issue is.
 
It likely has to do with overloading the input gains with the low frequencies. I don't know the technical whyfor's, but most pedals will clip nicely until you get into the low frequencies, which will clip into over-compressed farting, and stacking pedals will often exacerbate the effect because one pedal is hitting the other with that much more gain. When you have something like the Bass Big Muff that is designed for a lot of clipping anyway, it can get messy stacking unless you stay high up on the neck. Only a few pedals I've tried are tuned such that they do not fart out on the low end with extra gain in front of them (Darkglass VMT and SolidGoldFX Beta come to mind).