Straight from Topps (emphasis mine):
Thank you for your inquiry. Please be advised, the Black bordered cards is a Wal-Mart exclusive.
To assist collectors in identifying the Wal-Mart exclusive “BLACK” cards in 2009 Topps Baseball Series 1, Topps is issuing the $19.99 Value Box’s 9-digit component code. This code can be found directly on the top of box’s bar code.
In addition, Target also has an exclusive $19.99 Value Box, which includes “THROWBACK” versions of 2009 Topps Baseball Series 1 featuring gray-back cardboard stock and the retro Topps logo. These boxes also have an identifiable component code found directly on top of the bar card.
The exclusive limited edition sets include each of the 330 subjects found in the 2009 Topps Series 1 Base Set. The codes are as follows:
Wal-Mart “BLACK” Cards
All the base cards found in this version of the VALUE BOX will be “BLACK”.
Target “THROWBACK” Cards
All the base cards found in this version of the VALUE BOX will be “THROWBACK”.
As always, please do not hesitate to contact our Customer Service team (By Phone: 800-489-9149, or by Email:email@example.com) if you ever have any other questions, comments or suggestions. A customer service representative will be available to answer your questions between the hours of 8:30am-4:30pm (EST), Monday through Friday.
The Topps Company, Inc.
First, I want to publicly thank Topps for answering my email AND for the detailed report as to what to expect. Second, this confirms that the cards are NOT errors as some thought - nor are they all that rare it appears. And now, that mystery been solved!