The mystery of the missing iPhones has reached a fever pitch, and several pundits including Piper Jaffray analyst Gene Munster have interpreted the shortage to mean that a 3G model is on its way to stores soon, bolstered, it seems, by the comments of AT&T (NYSE: T) Mobility president Ralph de la Vega at CTIA yesterday, where he hinted heavily—but did not outright confirm—that the iPhone would be on the 3G network within months. Others including Sanford C. Bernstein analyst A.M. Sacconaghi Jr., believes Apple (NSDQ: AAPL) is really just short of handsets. In an interesting response that surfaced on Saul Hansell’s NYT BITS blog on the missing iPhones, an anonymous poster put forth the theory that the runaway gray market for iPhones in emerging countries was making it difficult for Apple to manage its supply chain projections—hence the shortage.

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“Tantrum,” as the poster signed him/herself noted that 100,000 gray market units was to be expected, but with upward of one million iPhones going gray… “That’s a whole different ball game for component sourcing, quality control and production ramp-up and some things are starting to come unstuck, even for a finely managed company like Apple.”

This is not a wild theory. Since its launch, iPhone has struggled with gray market sellers in Europe and Asia, where they’ve played a whack-a-mole game of sending out letters threatening legal action against them. In February, there were reports that 1.4 million iPhones were unaccounted for—that is they weren’t registered on the respective networks they had been bought for. The post goes on to give a very detailed analysis of how American analysts can take a too US-Europe-centric view of the iPhone, all the while an organized gray market—with some sellers even offering support on the hacked iPhones—is catering to the wealthy elite in emerging countries. The upshot: a “conservative estimate” of 15,000-20,000 sucked out of the US on a weekly basis and ending up in China, India, Brazil, the Middle East among others just at a time when American iPhone adoption is ramping up even more.