2nd HDD bay with HDD = notebook won't boot with HDD in 2nd HDD bay

I recently came into a Pavilion DV9308 Notebook. It was in decent shape, well looked new and since I like tinkering with laptops and the motherboard had the dreaded NVIDIA GPU failure going on, I sent the motherboard out to my motherboard dude and he put a newer NVIDIA video chip in, made some adjustments and modifications to the heatsink cooler etc. Along with my modifications including vent holes and sealing up the fan blowing assembly so when the fan turned on the hot air would leave the laptop it now runs Windows 7 64 bit with a 64GB Kingston OS SSHD and 4GB DDR2 800mhz ram. It runs like lightning and impresses people when they see it boot up in 15 seconds.
The problem is and the whole reason I picked this notebook to restore is because it has two acutal hard drive bays. Well ever since I've gotten the notebook It will not boot with a hard drive in both bays or a hard drive in Bay #2. I had to send the repaired motherboard back once because one of the ram slots wasn't working so this is happening on two different motherboards. I cannot find a reason why this is happening and have yet to find anyone that can help me with this. Can anyone explain to me what I'm doing wrong? I have all the correct drivers I think and the laptop runs at 130"F when pushed to the max! That is amazing compared to what it originally ran. It would be awesome if someone could please help me with this. Thanks.

Hello jason9922.  I understand your notebook won't boot with a hard drive in the second bay.
When you say that the notebook won't boot with a drive in the second bay what exactly do you mean?  Does the CAPS LOCK key flash or do you get an error?
When you have the hard drive installed can you access the BIOS?  If so, is the hard drive detected within the BIOS?
I'll keep an eye out for your response.  Have a great day!
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