When you install Windows, it created a unique SID for that specific machine. When you add the licence code to Windows, it ties that to your SID.
If you clone a machine, you're duplicating the SID and licence combination, which will result in the message you're receiving.
When you start up the clone while the original is running, Windows phones home and "realises" that the SID/licence combination is being used twice. It then notifies you, quite correctly, that you're breaching the single installation licence for Pro.
Your only solutions are:
1. Run one machine at a time.
2. Buy another licence.
3. Move to Enterprise and build a KMS Server.