Is your phone number checked even though it is grayed out? It is chosen by default and even though grayed out should be checked automatically. I had the same issue with people getting my messages from my icloud email which I never use and my messages would start new threads because of it and some people did not recognize my email. Well, one thing that helped me was to go in and make sure that the email you use for your Apple ID is listed as "Home" in your contacts on each of your devices. I'm not sure if that is working with everyone I am messaging yet, but it solved some of them.
Also for me, I am not getting iMessages on my ipad or MBP with Mtn Lion. I have not solved this yet. Anybody out there had this issue yet?