Mavericks (10.9.5) time machine and server 3.2.1 user permissions conflict

We are using a Mac mini Server (mid 2010) 2.66 GHz Intel Core 2 Duo, 4GB 1067MHz DDR3, NVIDIA GeForce 320M 256MB machine. There are 2 500GB hard disks which have each been partitioned into 2 separate logical disks of 250GB each (in total 4 logical 250GB disks).
We having been using this server to file share on the local network for years using Snow Leopard, Lion and Mountain Lion (although there were teething problems with Mountain Lion using the new Server app).
After experiencing some issues with an iCloud password change and App Store failing to load, we decided to try updating to Mavericks. Upon update we were prompted to update the Server app to Mavericks version (Server app 3.2.1), this seemed to work to begin with, preserving file sharing and network user records and permissions, however we soon started to experience issues with permissions and Time Machine. We noticed that the Open Directory set up to store our network users was no longer available in the Server app and so decided to erase one of the alternate partitions and perform a clean install of Mavericks and Server app 3.2.1. This proved to produce the same issues with Time Machine permissions and also difficulties with the shared folder permissions.
Any help with this would be greatly appreciated.
Thanks

Hi Linc,
Thanks for the reply.
The Time Machine folders shown are from the Server app Storage tab which shows all connected hard drives. I haven't set TM drives up to be shared and hopefully the following screenshots will illustrate the current setup. This setup was created from a clean install of all involved software i.e. drives were erased and setup from scratch and the TM drives were simply connected and TM took control from there.
As you can see from these screenshots, when viewing the permissions through the Server app, there appears to be an extra user when compared to the OS Get Info window.
After leaving TM to its own devices over the weekend, I was greeted with a 'preparing backup' message this morning(Mon 13th October), with a last backup completed on Sat 11th October at 15:19:16. Stopping this backup and starting a manual backup has now resulted in a new, never before experienced error message stating that the backup disks can not be found:
Console reports:
I must re-iterate, the disk was erased and simply connected and Time Machine did its thing. Now as 'admin' it is clear that the folders created by TM do not have permissions so that I can simply view them in Finder, but does this directly affect TMs ability to access folders it has created itself?
One useful bit of information I seem to have neglected is that the erased TM drive is encrypted, however the password was entered when the drive was connected to the machine and there has been no prompt thereafter.
Please help. Only other comment I can make is that before the update to Mavericks and Server app 3.2.1, none of this was a problem.

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