Don't forget that the stock Hyperion balancer plugs are wired a bit oddly. For example, for a 2s pack, the balance connector has 5 wire positions, but only three are used. The wire order is red (most positive terminal), black (the tap between the two cells), and black (the most negative terminal). The red and black are right next to each other, while the last black is two connector positions away. See the diagram below for a more graphic example.
You can verify wire order by taking a voltmeter and placing the negative probe on the far (lone) black wire. Then, with the positive probe, measuring the next black wire will read ~3.7v. The red wire will read ~7.4v. This is the correct order. If you do not have those readings, the order is incorrect.
Also, look at your connectors. Wherever a connector position contains a wire, there has to be a wire coming out the other connector in the same spot.
Maybe a clear picture of your setup would help...