you statement that the varying lots caused the wash sale gives me pause. did you happen to buy that same stock again within 30 days of the sale? if you did, then THAT is what is driving the wash sale .
selling shares by themselves when you close out the position (purchase 2000 shares and sell 2000 shares) doesn't by itself create a wash sale
example:
1) buy 2000 shares @ $10 on January 2
2) sell 2000 shares @ 9 on January 3 (capital loss of $2000)
3) buy 2000 @ 8 on January 4 (wash sale - capital loss must be deferred)
that is a wash sale. the losses that occur on January 3 can't be taken until the lots purchased on January 4th are sold.
