MSI 890FXA-GD70 solid red HDD light and tower power button not functioning properly.

Hello all, I have recently come across some issues when I rebuilt my computer and can't seem to figure them out, So I will just start from the beginning with what I did, the issues, and what I have tried thus far.

What I have recently done to my system:

So I recently bought a new tower (Thermaltake Chaser MK-1), graphics card (EVGA GeForce GTX 970 2GB), and a SSD (Kingston 60GB). I wanted to upgrade my tower due to broken fan control, the graphics card because my old one was out of date (EVGA GTX 570), and the SSD to use as a boot drive as I was previously booting off of my one and only drive in my tower.

I got everything installed just fine, or so I thought. Once I completed the install, I got ready to boot it back up to format the SSD and get ready to install windows 7 onto it. Sure enough the power button on the tower didn't work. My first though was I messed up the pins for the tower controls. So, I took it back apart and inspected. All the pins were correctly installed. At this point I just wanted to get booted up and get windows and all my drivers installed, so I manually powered up via the on-board power button.

I didn't have any issues formatting the SSD, installing windows, or the drivers, so my only problem became the towers power button. (I also changed the boot order in my BIOS so the SSD was second only to the DVD drive). Seemed to work just fine, and I still don't have any problems with the booting of my system as long as I manually power up via the on-board button.

The Problems:

My first problem is the power button. It still wont power on my machine when it is off. However, if I manually power on, the power button starts working. I can shut down my system via the button, and if I recently shut it down, the power button on the tower will power it back on. Quite perplexing to me, but I believe this confirms that the towers button leads are indeed plugged in correctly. Any ideas what could be causing this?

Second, now that my new tower has a window in it, I have noticed a constant red light coming from the motherboard (MSI 890FXA-GD70). I honestly don't know if this was on before I rebuilt or not since my old tower did not have a window. Upon inspection I found that it was the HDD light that was a constant red. I've checked the manual and it actually doesn't even show a HDD light in it (page 47). I've done some googling and searching this forum and have found that most people think it would either be misplaced plugins on the board or a bent piece on the board. The bent piece could be a possibility as I did jumble one resistor (I think that what it was) when I was removing my fan plug ins during the re-build, but it was VERY minor. I have also tried resetting my BIOS settings to their default and the other option (safest default or something? It's slipping my mind right now, sorry). Both of these default settings result in my system not booting at all. It tells me it cant find windows or something like that and won't boot. So, I changed my boot order back to what I had it and it boots fine again (as long as I manually power it on). Here is my current boot order:

1 - CD/DVD: 4M-HL-D
2 - SATA: 45 KINGSTON (my SSD)
3 - SATA: 3M-WDC WD (my alternate hard drive that I formatted completely after I installed windows to the SSD)
4- USB: WD MY BOOK (an external storage device)
5- USB: WD SES DEV (I actually don't know what this one is, possibly my wireless mouse/keyboard?)
6- USB: HP PHOTOSMART (my printer)

I was thinking maybe if I didn't have the usb devices plugged in when I established the boot order? But I figured it would just auto put them in anyways the next time I start my system.

So, all in all, my two problems are power button not working and the solid red HDD light on my motherboard. I would hope that they are related somehow and have a quick fix. Any suggestions guys?

I also just bought a Samsung 250GB SSD that I will be replacing the 60GB one with today, or very soon because of space issues that I will be posting to the hard drive forum, so if you want to give me even more help, head on over there! Thank you very much for any assistance, I greatly appreciate it.

Here is my full component list if it will help:

Motherboard: MSI 890FXA-GD70
Processor: AMD Phenom 2 X6 1100
Heatsink: A very large two fan / two radiator heatsink (model unsure)
Memory: G Skill Ripjaw Series 16GB (2 x 8GB) DDR3
GPU: EVGA GeForce GTX 970 2GB
SSD: Kingston 60GB (current boot drive)
Hard drive: Western Digital 1TB
DVD: LG blueray player/burner
Power supply: Antec 750 Watt

If anyone needs any additional info, I will be more than happy to provide it.
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