Check that your Caller ID isn't set for your Apple ID. If it is set for your phone # yet still coming from your Apple ID, there could be two reasons for this...
a) Your last conversation with that person or persons was done over your Apple ID and iMessage keeps the conversation with that Apple ID until you delete it.
b) Change the Caller ID to/from your phone number, then back again. This will reset the Caller ID for iMessage.
I've been using it since iOS 5 launched and it's saved me a ton on international SMS, very pleased with it. However, there were glitches (like this) when it first launched. Thankfully, they've cleared up most of them in subsequent updates.