Ssd not detected in 6gbs port

I just got my new intel ssd today. I unplugged my old hdd and plugged in my ssd. My motherboard has 2x6gb/s sata ports and 4 3gbs sata ports. I plugged in my ssd into the 6gbs sata port and turned on my computer and went into bios only to find out that my ssd wasn't being detected.

I took it out of the 6gbs port and put it in the 3gbs port and it worked. So, I proceeded to install a fresh copy of win 7. After I installed windows 7 and all of the drivers I plugged my hdd back in. I plugged it into the 3gbs port. For some odd reason it won't recognize the hdd. So I went ahead and unplugged the ssd and left the hdd in and booted it up. This time bios detected it.

There is probably a simple way to fix this but I don't know how to properly ask the question in google so I am here asking the community.

How can I fix this?
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More about detected 6gbs port
  1. Update***

    I cleared CMOS and now my ssd works in the 6gbs ports.

    I still can't get my motherboard to recognize my old hdd though. The HDD was always working before I installed this ssd.

    I changed sata cables and plugged them into different ports but my hdd is still not recognized.
  2. everything works now. seems like clearing the CMOS fixed everything.
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