Okay... with a lot of too'ing and fro'ing with Konstantin (*high five*) from Veeam support It is now working. A quick summary on how to do this is below for those that need to do it (you will see why you really would have had no hope figuring it out yourself)Before you start the below, domain authentication is suppose to work but i couldn't work it out. The format is suppose to be %domain%_%username% for the folder you create in step 1 but i couldn't make it work, so i dropped back to using a local user account which does work.
1) Copy backup folder from original server to a VBR 9.0U1 repository. This part is is important, it wont work with any lower version. Now to do this you need to create a folder off the root of VBR repository in the format of %VBRHOSTNAME%_%VEB_TO_VBR_Username%. So, using mine as an example, my VBR host is called ARBBackup and the username that I enter into VEB to connect to the VBR repository is 'ARBComp'. So the folder that I create is called "ARBBackup_ARBComp" In that folder just copy the seeded backup directory. In my case the folder is called "Backup Job SADC1" so if my repository was located in F:\Backup I would have to create the following path "F:\Backup\ARBBackup_ARBComp\Backup Folder SADC1" which would contain the backup VBK and VBM files.
2) Re-scan the repository. The imported backup is now shown in the repository under “Backups -> Disk (imported)”
3) In VEB configure the jobs properties as before. In my case I am backing up the “Entire Computer” to a “Veeam Backup and Replication Repository”.
4) Select the VBR repository and set any other options you wish.
5) Select Save / Finish
6) Now at this point you NEED to see that the backup has moved from the Imported section to the normal Backup (Disk) section with the rest of your backups. If you don't see this then the seed wont work, it has to move.
7) Re-scan the repository. You wont see any changes here... just do it, as it updates the Veeam DB with metadata file, failure to re-scan will throw an error at the VEB end which will result in the backup not running at all.
Start the job
9) Checking the VEB job log you can now see that it is running in incremental mode
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[21.04.2016 15:10:00] <01> Info Job session is running in incremental mode
10) Have a well earned drink.
Depending on how big your backup file is this may take a while the first time as the metadata needs to be checksummed and the changes transferred which depending on the speed of your link.... may take some time.
If anyone has any questions on this please do let me know, i've had a rough ride with this feature but have a handle on it now.