Sounds like some small rocks were in the coffee. Big rocks would have bound up the burrs. The inconsistencies would come from the damage the little rocks did to the cutting teeth on the burrs and would even out after a week or so of grinding through more coffee. Have you taken the burrs apart and cleaned the inside of the grinding chamber? You might want to take a look and see if the burrs look damaged at all. You should be cleaning out the grind chamber at least weekly anyway.
+1 on the rock. This is extremely common (especially with Papuas). I'd be willing to bet that it's accompanied by a small amount of tiny white particles in the ground espresso. Not much you can do about that except to do a quick visual on the espresso as you're filling the hopper. You might also try keeping a small shopvac ($25 at Lowes) handy, turn off the grinder as soon as you hear the noise, remove the hopper and suck out the grind chamber quickly. If you know what you're doing, you can do this and be back to pulling shots in under a minute. Small price to pay to extend the life of some expensive burrs.
I'm also with Mike on checking your burrs - rocks will certainly reduce their life.