I can't make a case for why the USB card could be the cause of the problem unless, there is a design or physical problem with the motherboard itself.
The pinout that I have for the PCI connector does not reference any of the lines as a battery line.
That said, what I would do is check for voltage on each pin with power off, and see if there is battery voltage present.
If there is, then there is a problem with your motherboard.
If there is no voltage on any pin of the connector, then it is just a coincidence that the battery started failing after you installed the card.
Check for a date code on the next battery you purchase to assure that it is not already several years old.
Another thing you could do, is to check the current drain on the battery with the card in the board, and out. If the current drain is constant, then the USB card is not the problem.