Yeah, it's importing short transactions weirdly. Instead of importing sales proceeds as the proceeds from selling short and cost basis as the cost of covering, it is importing the net profit / loss from the position as the sales proceeds and leaving the cost basis field blank. You can manually correct proceeds and basis on each transaction, or you can just put a "0" in the basis field and TT is able to manage it. I'm no accountant, so I can't comment on how the IRS would feel about option 2 (reported gains are the same either way). At least this is the specific issue I ran into.
