Dear Hari,
Department is often wrong in interpretation of data received by them. This is specially true for capital gains, cash deposits. We have seen in multiple cases where same transaction is reported to them multiple times and they just add it up. in one case, same sale of a house was counted up 6 times and added to the income of the assessee.
You need to be very diligent about how you reply to such notices and ensure that the Income-tax department understands the correct position. If not dealt well, it could lead to significant demand plus penalty proceedings. Other day itself we had a query where penalty proceedings were issued despite no addition made in the reassessment proceedings.
Take professional help if you can afford.