When I type in the 1099 B information my federal refund increases as opposed to when I import the same information from TD Ameritrade. Yes the numbers are the same...

[Country Apple]

Perhaps you are incorrectly selecting a long term holding period as opposed to a short term holding period.  The  direct downloads are usually very accurate.

[DanP0428]

The difference is probably in the basis field.

[wfabrie]

There were several transactions with a capitol loss, so I'm wondering if the totals when imported do not reflect that?  

[wfabrie]

Nope, correctly selected the appropriate holdings.  Wondering if the import did not since there were 3 separate holding definitions?

[Country Apple]

I would double-check each transaction to make sure every transaction has cost and sale information and that the input is the same as the 1099.  Also make sure dividends and interest have been included.  If you're dealing with employee stock option transactions, you will need to adjust those costs.