Hi,
How big are the data discrepancies?
Whenever I compare Data Warehouse and Workspace/Reports I always find a small discrepancy but have found that this is usually explained by the fact that Data Warehouse holds unprocessed data compared to the processed front end data you see in Workspace/Reports, so we accept a small difference.
I've never had a Warehouse extract fail on size as long as the FTP Server I send it to has enough space, are you requesting it via email?
Thanks,
Paige