Ages ago, I had a similar problem, and I can't replicate it now, but, if you go in the organizer window and look up your device, sometimes there's an option to "enable device" or something like that. I'm NOT talking about the "use device for development" feature which is new in xcode4. It's just, once, I had a device somehow become unrecognized by xcode, and, digging around the organizer window, I found an option to do something like reconnect the device, and that fixed it. This was a long time ago so I don't remember anything more than that. (Right now, I notice that, if I go in the xcode window and right click on my currently connected device, there is an option to "ignore device", so maybe that's what got turned on way back when.)
Here are some other ideas:
*) Have you tried "untweaking" your project settings?
*) Have you cleaned all targets?
*) Different cable?
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