If you've made them, do you end up with crunchy bits in the batter? It must be unground grains, but I can't imagine why they're not ground up completely.
FWIW, I use my super-awesome better-than-a-blender food processor instead of a blender, and I run it just about forever before and after soaking. I'm making pancakes, not waffles, but I don't think that's where the problem lies. I've done it twice, once with buckwheat and brown rice, and once with buckwheat and amaranth, and had the problem both times.
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