There was a performance degrade for the SQL connector which was discovered in release 6.1 IR and fixed in release 6.1.1.
In release 6.1.2 there was a significant performance improvement for the SQL connector. We noticed up to 30 % better performance when extracting from some SAP tables!
If possible, I suggest that you upgrade to the latest released version 6.3.2. In the near future release 6.4.0 will also be available.
Thanks Hakan - I think this will be the steps I need to take. Whilst I'm sure it will improve performance it might not resolve the initial cause of the problem of 5 +fold increase in extract time. I'm assuming coming from 6.0.xx, I'll have to also redeploy SAP transports to support the 6.3.2 connector.