Im having an odd issue with a pair of iphone4 (Black/White | Orange-O2 carriers | iOs5) i have.
I recently baught one new for my partner and set it up through a copy of itunes i have my own Iphone4 synced with, i also signed in with my itunes account to add some of my own purchases to the device, then signed out and gave her her own apple id.
The problem is that the two devices dont seem to comunicate properly through either carrier or Imessage.
When my partner sends me an Sms it displays "my email address" as the sender, even though i have my partners number stored in my phone already and she doesnt seem to receieve any messages from me.
This doesn't have anything to do with iTunes. It sounds like its either a carrier based problem, or your settings for email/SMS got blended somehow. You may try to reset all the defaults on both devices and see if that helps. BTW welcome to PinStack.
Be sure you have enabled iMessages in setting also. That has to be turned on.
On another note since you posted about it. Did you install Apps under your Apple ID on the new device? If so then signed in under a new Apple ID on the device I don't think those Apps will work. You can't share Apps under different Apple ID's.