Hi Vinny,
Can you confirm that on the iPhone you can "Send " to the Apple ID when you have the iPhone set to Start conversations From the iPhone Number ?
In this particular case you should see a "Send" and a "Receive" version as the Sync with the Apple ID should cause this.
Also does the iPad see the iMessage ?
If you use the Contact item top right of the Conversation you should see the ID (or iPhone number) that is in use indicated by it being blue when looking at the Address Card.
Next on the iPad disable the iPhone Number so it will only get Apple ID iMessages.
On the Mac version do the same.
On the iPhone set it to "Send" from the iPhone Number and iMessage the Apple ID.
This should exclude th Sync Process confusing what is working or not.
Which Devices does it show up on ?
On the Mac version whilst the iPhone number is still deselected (as a Sync option)will it send any iMessages to your iPhone Number ?
From what I understand this is not happening even when the app looks logged in.
If this is the case shut down Messages and open Finder Window.
Use the Go Menu > Go to Folder and enter ~/Library/Preferences into the dialogue box.
Once in the Preferences folder find the following:-
com.apple.imessage.bag.plist
com.apple.ids.service.com.apple.madrid.plist
Drag these both to the Trash.
Restart Messages.
The first of these holds the Server info, the second holds the the Apple ID and any "Aliases" set up with the account (which should include the iPhone Number)
Messages will probably need resetting with the Apple ID.
Before doing anything else on any device test whether you can send to the iPhone Number.
If this works then turn On the Apple ID option on the iPhone.
Restart the Mac version and you should get the Pop ups saying what the iPhone is using.
Accept these and the iPhone number should be added to the iMessages info.
Re-add the Apple ID to the iPad. At some point this should also generate Pop ups on the Mac and the iPhone to confirm what the iPad is using.
7:31 pm Wednesday; July 9, 2014
iMac 2.5Ghz i5 2011 (Mavericks 10.9)
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