What type of thread are you using? Some types tangle more easily than others. Regular Nymo used to make me SOOOO mad with some horrendous knots no matter how much wax or thread heaven I slid on. I've had better luck with Silamide behaving like it should.
Basically I take up a lot of space, and stop every couple of beads to hang the needle letting it untangle. As I stitch the beads, I try to take arm lengths of the thread and lay it fairly flat next to me. I'll also try to run my finger between the extra "tail" beyond the needle eye and the line between the project and needle to help keep things separated. Every few bead stitches, I will hold the thread near my project and let the needle dangle so it will spin and "unwind" to help keep the tangles clear.
Is your needle bent? For some reason I twist my needles more as they develop what I call the project curve.
Maybe a new needle will help?
You are on the right track by keeping your thread well waxed. Maybe try some extra wax here and there in the middle of the project? Same deal as prepping the thread- slide it through, then use your fingers to clear off the excess along the line.
Finally, sometimes I just have to use a shorter thread and deal with weaving in multiple tails throughout the piece. It seems like such a pain, but if you think of all of the time spent untangling the super long thread, it can be better in the long run. Needy darn projects!
Hopefully something will help you out. I can't wait to see how it looks when you finish!