Thanks for the advice and help i think I have enough info to get this working.
I recently purchased 2 Seagate ST31000524AS drives which are a newer version of the ST31000524NS which is listed as compatible in the MD1000 matrix to use as hot spares in our MD1000 and got the following error after inserting the drive. Bad PHY Slot4 Physical Disk1:2 Controller 1 Connector1 Does anyone know if these new drives are incompatible with the MD1000 as I get the same error with both drives.  
MD1000