All of a sudden, customers in the U.S. are finding it a lot harder to track down an iPhone.

A few weeks ago, New York iPhone shoppers noticed that Apple’s Manhattan retail stores were running low on iPhones. Gene Munster of Piper Jaffray, during an intermission in his three-part series on why Apple is the coolest ever, called up 20 different Apple stores across the U.S. and confirmed that the shortage extends nationwide. Apple’s online store reports a five-to-seven-day wait on iPhone shipments.

There’s usually a couple of reasons for a product shortage. One, demand is outstripping the ability of a company to supply the product. That’s probably not the case here, since Apple’s had no problems supplying iPhone demand since the initial weekend it went on sale, and there’s no indication that demand has spiked in the last couple of weeks. Apple did announce the iPhone 2.0 software in early March, which might have pushed a few people over the edge, but the software itself won’t be available until June.

Two, a glitch somewhere in manufacturing or the supply chain is screwing up distribution. Munster assigns a 20 percent likelihood to this possibility; there might be a problem with the touch screen or other sensitive piece of equipment that hasn’t come to light yet.

The third reason is that the company is intentionally clearing inventory ahead of a new product launch. This happens all the time in technology; in Apple’s case, we saw it just before the launch of new MacBook Pros in late February. Munster gave this possibility an 80 percent chance of being the cause behind the shortages.

The 3G version of the iPhone is what everyone is waiting for, and the inventory problems might be an indication that it’s just around the corner. There have been scattered reports of a 3G model arriving anywhere from May to September, but if the inventory problems are really related to the pending launch, that means it could be here a lot sooner.