This was never a polarity issue. One of three things is going on here:
1) You have a short circuit somewhere, accidentally connecting two of the LED lines
2) You have an open circuit– missing a connection between the LED lines and the (right) LEDs
3) A damaged LED. It may still light, but may have very different voltage characteristics than its neighbors, which would cause the effect that you see.
If you would like to test with the power supply, apply the 5 V (with a resistor) to lines LED10 and LED2. If you would like to test to see what happens if you remove the red LED without actually desoldering it, you can clip one of its two leads between the circuit board and the LED body, and separate it just a small amount so that it doesn’t touch. Then, touch a new red LED across that point to see the effect of putting a new LED in that location. The LED lead that you cut can be repaired by bending it so that the two cut ends touch, and putting a tiny dot of solder between them.
And, if all else fails, you can send the clock — in its current state — back to us for us to take a look at it. If you would like to do that, please use our contact for to request an RMA.
