Hi,
Each Messages app and then iMessages accounts needs the Serial Number of the Mac to be Present to create the Auth token needs to login.
In the Keychain (Applications/Utilities and open the Keychain Access App) is an IDS: yourAppleID@someEmailServer.com-Auth Token item.
If it is not there the iMessages Account cannot login.
Whilst you may use the same Apple ID in iTunes/App Store, FaceTime and iMessages, Game Center or even iCloud itself they all login in to different servers.
If you use a VM like this iTunes/App Store will regard it as one of your 5 "registered" computers.
However as iMessages creates the Auth Token duplicates can be an issue.
Each Device has a specific Registration with the iMessages servers (it means the iMessages are sent individually to a Device - which in turn means the Read and Delete type "syncing" people expect does not work.
You can check the Serial Number is on the Computer by going to the Apple Icon Menu top left and then About this Mac.
In Mavericks click twice on the line that tells you the OS X version.
The first click reveals the Build Number (another way Apple Counts the OS Versions) then the second will show the Serial Number.
A Clone as the VM version might have this details but this will cause issues at the iMessages server as it will appear the same device is trying to login twice - which in some senses it is.
A Fresh Install as the VM version is likely to be missing this info and the Login will be rejected.

7:48 pm Friday; March 6, 2015
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