Nozzle failures in the field! Time for a little nozzle dissection to see what’s going on.
http://www.jerrill.com/blog/2013/04/whats-in-a-nozzle/
Are you using a lathe to make these?
You can set up a depth gauge to gauge the thickness before you cut. You can then set a threshold for usable/unusable and determine how much material needs to be cut for the flat. Note that printrbots configuration is ideal because it will give a stronger nozzle and less material in the melt zone.
@Stephanie_A the influence of the length of the melt zone is much disputed - Budaschnozzles, for example, have a 30mm long melt zone, but still print nicely.
@LulzBot published drawings of the Schnozzle, which indicate a .5mm depth of the nozzle bore. This is the same way I bored my nozzle as well - the trick to keeping strength high is to have a steeper angle on the inside (filament-sized) bore than on the outside, like the MakerBot nozzle. This way only material right next to the nozzle hole will gave that .5 thickness, while the outer regions will be thicker. Not much of a choice with acorn nuts, though…
@Stephanie_A My setup hasn’t changed too much from when I made this original video for the nozzle toolbox I posted on Thingiverse - http://youtu.be/kYImCO_SDms . I’ve replaced the printed chuck with a real mini chuck. I’m getting ready to replace the hand drill with a dremel tool to get the drill bit speed up for smaller nozzle bore diameters. I’ll give the depth gauge a shot this weekend and see if it improves the downstream fallout. I keep hoping for the day that I can justify getting the blanks manufactured, but that day hasn’t arrived quite yet. The project is self sustaining at this point, but not to the point where I would quit my day job or anything. And it would pay for filament too, but I’m not using much printing out all these tiny things. 
It would be sweet to have some of those super tiny nozzles in http://www.lulzbot.com/?q=products/budaschnozzle-11-nozzle-no-hole-blank
The difference is that the printrbot and makerbot people start off with hexagonal bars, and do multiple machining operations on them. They use a lot more material, but the quality of their ends is better for it.
A few things that might help. A lathe will give you precision cuts and drilling. My personal choice is sherline.
Second to that, you can get a drill press for pretty cheap.
The acorn nut should be the rotating piece while the drill bit is held stationary. You will get more accurate holes and break less bits that way.
You could also design a mini lathe using off the shelf components, but you are looking for high tolerances if you want high yeilds.
Thanks for posting the pic of the cut nozzles. Looks like the pb nozzle uses two passes and the mb nozzle uses a custom bit.
@Stephanie_A I’ve been thinking about what you said about holding the bit stationary and turning the acorn nut. Someone else on Thingiverse had recommended the same thing. But I’m having a hard time imagining how that would break fewer bits. It seems that unless the bit landed on the rotating nut at the exact axis of rotation it would be more likely to break because it would effectively be dragging on the rotating nut. At least with the stationary nut, I can land the bit anywhere on the flat and have a chance at getting a hole. What am I missing? Thanks.