Magnetar_Byte

Hello,
First of all, each connector that has an LED is polarity keyed because LED powered connectors need a + and - to transmit voltage signals to the front I/O for the lights.
The HDD LED and Power LED are both polarity keyed.
So what it means is, Pin "1" for HDD LED has positive polarity and pin "3" for HDD LED has negative polarity.  So that's where the pins go.
Pin numbers on circuit boards are *usually* counted CLOCKWISE for chip IC's (like SOIC8 or DIP8 chips). 
However there seems to be no clear standard for how they are labeled on jumper pins.  
 
In your example, you have them labeled wrong.  In this case, they are staggered in groups, so pin 1 is bottom left and pin 2 is top left, then pin 3 is to the RIGHT of bottom left, and pin 4 is to the RIGHT of top left!
 
So your label is wrong.
Please don't make fun of my paint skills.  I have zero artistic ability.  But this is how they are supposed to be labeled.
They mark "1" and "8" so you know where to start and stop.
So as you can see, pins 1 and 3 are HORIZONTAL orientation on the rectangle sideways (long way).  So HDD LED pin "+" goes in the bottom left, and the "-" pin goes right next to it
 

This makes much more sense. I was gonna say I get my case and Mobo are from diff companies. But I couldn't imagine it would be that different, i'll try it hold up.
 
And thxs  my paint skills are just as bad lol don't feel bad.