Dang, nothing worse than running into a problem right when you think you're done
Perhaps due to ebony being so hard as well? Maybe it needs just a couple thousandths more than other woods on the pre-drilling/reaming.
Another possibility is that the ebony is already under stress, so it cracks more easily. Its moisture expansion rate is so high, the water from the glue would expand it out a lot. Then after drying, it tries to shrink, but it can't. I've actually worried a bit about that, since I also put water on the outside of the headplate to equalize expansion and prevent it from curling away from the surface while I get it clamped. That's a lot of expansion during glue-up, which translates to a lot of stress trying to curl up the headstock or crack the headplate after it dries.
I've never actually used press-fit bushings before, but I will be on my current batch. All rosewood headplates though, and I'll be using a tapered reamer rather than the straight StewMac tools, so the pressure will be on the headstock wood further down the hole rather than the headplate.