Check for Organisations with your practice name
Before starting GP2GP, from Control Panel - File Maintenance - Organisations, check that you do not have an organisation set up with the same name as your practice.
For example, your practice may be called The Medical Centre, but if you also have an organisation within Organisations called The Medical Centre (this is usually left over from Fundholding days), GP2GP cannot distinguish which organisation the department is linked to so the hospital is not sent through and is therefore missed from the referral screen at the receiving practice.
So if there are any duplicate names within Organisations, edit one of them. In the example above, the General Practitioner Fundholder name could be changed to The Medical Centre old.