HI,
In the Mac version of Messages Sign Out of the iMessages account and Quit the app.
On the iPhone remove the Apple ID in Settings > Messages.
Place the iPhone in Airplane mode for 5 mins (break with server)
On coming out of Airplane Mode check Messages has the iPhone number ticked before re-adding the Apple ID.
Check both are ticked as Receive At and Send From options. (also reset your Send From choice).
Now restart Messages on the Mac.
Re-add the Apple ID
Accept the pop up(s) that tell you the iPhone is using it's number and Apple ID.
Realistically it's a Basic Reset everything.
8:02 pm Saturday; October 26, 2013
iMac 2.5Ghz 5i 2011 (Mountain Lion 10.8.4)
G4/1GhzDual MDD (Leopard 10.5.8)
MacBookPro 2Gb (Snow Leopard 10.6.8)
Mac OS X (10.6.8),
Couple of iPhones and an iPad