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I'm using an MSI P7N SLI Platinum Motherboard and my OS is Windows Vista Ultimate 64bit.

 The problem is that when I hook my headphones into the front input (which is on the top of my particular case) I can't get the headphones to work properly. They test properly and everything, I switch them to the primary output in the Audio Manager, and it still sends the Audio through the speakers.

Even though you enable the front output unless you have the option ticked to disable rear audio output when front is plugged in then both sets will work. 

Open up the realtek control panel go to audio I/O, there is a little wrench icon in the analog input section click on it.  Tick the mute rear panel output when front is pugged in option.  Usually this defaults like this but yours may not have???

Which audio manager are you using windows or realtek??? 

Great, they work now, but they are backwards. Left is right and vice versa WTF?

That means the front audio jacks are wired to the motherboard/soundcard wrong most likely.  Recheck your wiring.

I now can't get the mic to register my voice, even in the rear port. In the rear port in will register taps and such, but won't pick up any other input.

you might try enabling microphone boost. Should be a tick box in windows mixer or a link tool in realtek mixer.  Did it work before???  Not sure if you have realtek or not. 

Sigh...for some strange reason I plugged my mic in again to try that, after having reset and replugged many times, and it works now. Hopefully it will stay that way. I still hate the Realtek audio manager though and it still doesn't use my front panels right.

If your case only has the AC97 front connections then you might need to enable AC97 in bios.  As you said if they are backwards(left and right channels) then they are not hooked/wired to the motherboard properly anyway.  Are they still backwards or did you check the wiring???  

What is the case you have and did you build the system?????  You will have to determine if the front outs are HD cmpatible or just AC97.

The case wiring should be labeled but you need to check you motherboard manual for correct wiring to it.

 

EDIT- didn't see option to enable AC97 so hope your case is HD.  Just make sure they are all in correctly.

  Also I noticed your front audio panel connector is a little confusing compared to mine??  Looks like mine is plain old AC97 and yours is HD.

9    7  5  3  1

10   k  6  4  2

K is KEY or empty spot

(YOUR MANUAL)

1 MIC_L Microphone - Left channel
2 GND Ground
3 MIC_R Microphone - Right channel
4 NC
5 LINE out_R Analog Port - Right channel
6 MIC_JD Jack detection return from front panel microphone JACK1
7 Front_JD Jack detection sense line from the High Definition Audio CODEC
jack detection resistor network
8 NC No control
9 LINE out_L Analog Port - Left channel
10 LINEout_JD Jack detection return from front panel JACK2

Might have to open case and take a look at mine now as you have me wondering, but all works how I want it???

If your case only has wiring for AC97 connection then use below pins, really don't get the connects from your manual or on internet as I get jack detection with below connections.  Seems like you may have pin 5 and pin 9 backwards.  Basically same as above but with only single channel mic instead of left and right mic channels.

1 MIC in

2 GND

3 No connect

4 +5V

5 Line out right

6 No connect

7 No connect 

8 Key

9 Line out left

10 no connect.  

 

Got me confused now???LOL!!!!!!!!!