My YJ does the exact same thing. It's due for a tune up, as I haven't changed the plugs or wires since I built the engine in 04 or so. Misses just a little, on cold start up, and always goes away. It's my opinion that both our problems are more likely due to ignition than fuel. With throttle body injection, the fuel is delivered much like a carb. That makes me think that a 'rich' condition or a 'lean' condition would not give that type of intermittant miss. And all the electronics of the fuel injection system are simply designed to manage the air / fuel ratios. So a failure of the fuel injection sensors would simply make it run crappy with great regularity, not intermittantly. I could hypothesis that the condition is too rich at startup, but you should be able to smell the unburnt fuel in the exhaust. I suppose it could also be too lean at startup... dunno.
So I'm back to wondering if it's tune up related. Perhaps one of the (new) plugs or wires is got too much resistance, is improperly gapped, not quite 'clicked' on the nipple, etc.... or maybe the coil is getting a little weak, and isn't firing the plug when the engine first fires off (it's rich during startup). Maybe the 12v wire to the coil has some resisitance...