It appears whilst syncing the blockchain the computer halted resulting in a bad block at the top of the chain. After restarting no more blocks are being added and just repeated errors. There is probably a way to pop the top blocks off the stack of blocks and begin resyncing, is there a command for this with the new LMDB database format?
A sample of the error is: 2016-Oct-01 16:22:34.684999 [P2P3][104.168.166.221:18080 OUT]Sync data returned unknown top block: 1141839 -> 1148279 [6440 blocks (8 days) behind] SYNCHRONIZATION started