All of this is good advice! I would ALSO check your annealing cycle program. If that many of your beads are chipping, you may not be holding or soaking long enough. Or you may have such a deep dimple that no matter the speed of the rotary tool (mine is an old Craftsman that I have had since I was 14, and I am 48 now) you will get chips, just because of the angle of glass to steel.
If your dimples are deep, and you use 3/32" mandrels or larger, consider using a rod saw blade instead of a rotary tool. For me, half of a rod saw blade does a better job, is more controllable, and never chips my beads.
This is a rod saw blade -- just cut it in half at the middle with a bolt cutter or rotary tool cutoff blade, and you have two perfect bead reamers.
http://www.amazon.com/Stanley-15-410.../dp/B000FK5DH0 The only caveat is that if you are doing *very* delicate transparents you might want to use another method, because rod saw blades can scratch the glass when new.