I had the same issue with mine from the very beginning, which I bought on the in-store launch day. Kept thinking it was a software problem and there would be a fix soon -- but gradually I realized that *everyone* couldn't be having this problem or the boards would be burning up with complaints. So I started to investigate -- as noted, probably half of those having problems with the prox sensor traced it back to a screen protector.
Since I wasn't using a screen protector I had to dig further and eventually stumbled on a thread where someone mentioned that their glass wasn't sitting flush along the top edge of the phone, but was protruding above the top band where the earpiece is. My phone had the same problem, so I decided to *carefully* press it down a bit. Apparently it's secured with a strip of two-way foam tape under the glass (like the iPad screen) and the tape is a tiny bit compressible, so after applying pressure across the top edge of the glass for 30 seconds or so, the glass was flush or even a bit recessed. I tried a call -- and surprise, the proximity sensor worked exactly as it should.
Unfortunately this only lasts for a minute at most, because the screen soon returns to its original position. In the Sprint store, I think they thought I was hitting the crack pipe until I did the same thing right in front of them and showed them how I could make it work for a minute or two. They ran their "tests" and in about 20 minutes ordered me a new phone. It helped that all the demo phones in the store (which all worked) had glass that was flush with or lower than the top frame.
But yea, when I would move the phone away from my ear during a call, the phone would remain black.
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