I have similar tax problems. I imported my broker's e-file statements into Turbo Tax, then spent hours adding missing transactions and filling out missing cost bases or adjusting cases where the broker used FIFO where I had been doing different accounting in my own records. After spending many hours doing this and finishing after 2 weekends of work, my broker sent me totally amended forms - what a nightmare as I cannot just re-import them since it will wipe out my many manual changes. Also, I noticed the wash sales must have been accounted incorrectly by my broker, as they really should have a net 0 effect once all equities have been sold, yet the wash sales in their reported forms discounted much of my valid losses. The link below claims most brokers got the wash sale accounting all wrong - I asked my broker about that via their helpdesk and received a form response asking me to prove they are wrong. I am frustrated beyond belief and cannot use Mark-to-Market now since I have accumulated losses from prior years.

http://www.greencompany.com/blog/index.php?postid=139