I think this is one half of a similar problem that has been reviewed here and, I understand, is on the development team's to-do list. Transferring shares from one acct to another results in shares removed from one account and being added to the other acct. The remove shares are treated as sales @ zero cost resulting in incorrect capital gains/loss reporting, as you have observed. The add shares loses all history, including cost basis, etc., resulting in incorrect IRR and other related issues. I believe there is a feature request to handle this correctly that you can vote on?