You might try this.....
Sign out of your Apple ID on Mountain Lion Messages and your iPhone Messages.
Sign back into your Apple ID on your iPhone Messages. Make sure you have all the addresses you want to use for messaging (e.g. phone number, email address, etc.).
Sign back into your Apple ID on Mountain Lion Messages. Make sure you check all the same addresses as you did in your iPhone Messages.
The above should sync your devices and you should receive notifications in Mountain Lion and/or iPhone that the addresses you chose will be used. Check both Mountain Lion and your iPhone Messages to be sure both have the addresses checked that you want to use. Test the result by sending an iMessage from Mountain Lion Messages to your iPhone and reply back.