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I know nothing about GainsKeeper, but my experience with debugged programs is that when they misbehave it's GIGO.

Recall that two reports were created with GainsKeeper: one with the downloaded OFX data and one with data I imported manually from the "transaction history" area. The latter matches my records to the penny and is the one I will file. The nice thing about GainsKeeper is that it keeps track of wash sales, and with 1100 transactions it turns out there are a few.

The one time I was audited just over a year ago, it seems they had issues with my wash sale accounting. That year I only had one wash sale which I did not account for on D-1, but it netted out by the end of the year so accounting for it wouldn't have changed anything. At the audit I had all of my impeccably-kept records at my fingertips, including the tax return and all of the brokerage statements for the year in question, plus I made a spreadsheet demonstrating that it made no difference whether or not I accounted for the wash sale. Turns out I knew more about the wash sale rule than the IRS examiner. He made copies of my brokerage statements and as the weeks and months went by I received letters informing me that they had examined my return and would not be changing anything. Hopefully they will think twice about auditing me next time, as there is no low-hanging fruit for them here :-)
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