Ang - I guess my suggestion/question is to see if maybe you're under-plying the yarn? Remember that the yarn winding onto the bobbin has less twist in it than the plied yarn leaving your hands. Every time the yarn touches a point (the orifice, flyer hook, etc.), it loses just a bit of twist so in most cases, you should add more than you think you need. Also check the yarn on the bobbin occasionally at first to make sure it still has enough twist.
I tend to get a pretty balanced yarn when I navajo ply and if it isn't balanced off the wheel, a long soak in hot water and some vigorous handling/thwacking tend to even it out. I don't add much more twist for a navajo ply than I do for a 2-ply except in the first and last several feet of singles to make sure it doesn't drift apart when I'm starting. This is some fingering weight navajo plied BFL that's pretty much fresh off the wheel with no setting. It's pretty much balanced and setting the twist will make it completely balanced. I hope this helps.