Babylon, I guess I went negative on GainsKeeper's ability to adjust for short and wash sales too early. Since they say [...After your positions are baselined, GainsKeeper will automatically adjust your basis and gain/loss for all trades, wash sales, and corporate actions. Your Ameritrade export will not reflect short sales. When importing, be sure to identify all short sales by clicking on the appropriate "Short Sale Change" button(s)...], it looks that the adjustement, however painful, is a one-time process. Is that what you see?
Also, their ads at AT/Datek do not clearly say that the trial import only works for the first 25 transactions, so there's no way to test-drive it using a complete 2002 transactions file...
M_e