I apologize if this has already been answered. I didn't find anything in my search of the forums or FM help.
US tax law changed a few years ago to distinguish between "covered" and "non-covered" shares (based on whether the shares were purchased before Jan 1, 2011), and require detailed (lot/share-level) cost-basis tracking by the holding institution for covered shares.
Vanguard responded to this by separately computing average cost for covered and non-covered shares, and offering this explanation of how shares are handled in an account that includes both covered and non-covered shares:
"If you use the average cost method for covered and noncovered shares, Vanguard will sell your oldest (noncovered) shares first. Once all noncovered shares are sold, Vanguard will sell the covered shares. You'll also have two average cost figures—one for your noncovered shares and one for your covered shares"
I don't see an obvious/good way to handle this in FM. If I leave all transactions in one FM investment file, I don't get the same average cost that Vanguard will report, but if I separate transactions into two investments, I must split all distributions after Jan 1, 2011 (more work than I'm willing to do) to reflect true returns for the two sets of shares.
Any suggestions?