I've got an iPhone 4 at 4.0.1 jailbroken with jailbreakme.com. I've installed iTunes 10 on my MacBook Pro after DevTeam said it was okay. My device shows up fine and syncs fine. I know this doesn't help you fix your problem. Go to iTunes>Preferences>Devices. Does your iPhone show up in Device Backups? Check out this thread:
Apple discussing forum suggests a solution seems to be a more thorough re-installation of iTunes, including a proper removal of the Apple Mobile Device Support extension and receipt file.
Or do a Google search and find a ton of suggestions.