Thanks to you both for your replies.
The disk is not fragmented, we were testing this out with a brand new SAN attached disk to the server with no data on it. We thought originally it might be the tier of disk we were using, however we presented a tier1 disk (7+1 raid5 on 15k SAS) and it experienced the same performance profile.
Misaligned file systems are when the starting offset of the filesystem is not a multiple of 8 (most arrays have 32k blocks) so starting offsets of 32.5 means a single filesystem block will pass this boundary and result in two blocks being written for every single file system block. (causing a 100% write overhead)
We checked this on the other NBU server (at the other end of the VVR) by connecting a new disk to it and running the same test - it yeilded the same results. We then performed the same test on a server without SF and it performed very well - without the same write profile!
Supposedly 'three weeks ago' a failover test between the VVR nodes was performed (but failed) and we think this is when the performance issues started. I did not perform the test, and so what was done exactly is not known.