I have solved this problem myself.
As noted above I do not use Disk Quotas and I confirmed this via the OVM File Systems page which showed all quotas as zero (ie not used). The server in question had a complete fresh installation when V5 was released and as far as I can remember I haven't played about with disk quotas since. To check out if Disk Quotas were indeed part of the problem I set the quota for the user account used to access these shares to 1TB and saved the settings. The Windows shares immediately showed the changed to being allocated 1TB of space and now had some free space too. I went back to the Disk Quota settings and changed then all back to zero and saved the settings. Now the shares in Windows showed the full array size as I wanted and had plenty of free space.
As I note above I don't remember doing anything with the Disk Quota settings since the fresh V5 installation as its something I have never used before, nor should there have been anything carried forward from previous installs with a complete fresh installation. However resetting the disk quotas to zero has indeed solved the problem for me.