Tom,
Sounds like you most likely plugged the connector in backwards. They aren't supposed to fit backward but it doesn't take much to fit them that way. If you are using a JST-XH balance board, which is the most common, plugging in backwards is what you most likely did. This is one example of many http://www.progressiverc.com/safe-parallel-board-for-jst-xh-t-plug.html If you are using a Hyperion/Polyquest board Then you may have plugged it into a 2s or 3s slot accidentally (2s,3s, and 4s all use the same balance connector but they are wired differently.) That too would cause the issue that you described. Here is an example of the polyquest/hyperion board http://www.progressiverc.com/parallel-charge-board-for-polyquest-and-t-plug.html. Note the balance connectors look the same for 2,3, and 4s. The common denominator between the 2 types of boards lies at the 4s and higher slots. They are exactly the same on both boards. That's why I always recommend a JST/XH board for the hyperion 4s and higher as you cant make any mistakes plugging them in, unless of course you manage to fit one in backwards.