I wish I could give you an answer to what the problem could be for sure, but I can tell you that I have had SERIOUS discrepancies when downloading paypal information into quickbooks. I didn't notice it for a couple of years because I had a bookkeeper and the numbers seemed about right to me. But when I went to do my taxes the third year, the numbers seemed WAY off and had me owing about $10,000 more in taxes than I had anticipated. I had to go through the transactions line by line for the entire year and ended up with the numbers being where I thought they should have been. Over the course of the year, this was about a $40,000 discrepancy. We sort of figured out that the way that paypal names certain transactions, did not mesh with how quickbooks understood them and they were not downloaded into the correct accounts. You might try making sure that there is not an item missing from your quickbooks accounts that is not showing on your summary, or vice versa....like paypal fees or refunds.
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