Problem running 3TB mech HDD behing my new SSD

Ok...so I am having a odd issue and maybe you guys can help me. I just completed a new HTPC build. I was able to install the Corsair Neutron GTX SSD just fine and loaded Windows on it no problem so everything is peaches and cream. Since I am only planning on running the OS and programs from the SSD I bought a 3TB mech HDD that I plan to rip movies to and store all my media etc. I bought the Seagate Barracuda ST3000DM001.

After reading on the web I realized the way to utilize the full 3TB of the drive was to format it as a GTP drive. This worked just fine and now Windows can see the full 3TB but the problem is that now the system is getting confused between the SSD and the mech HDD. What I mean by that is that every time I restart the system it goes to the black screen with the blinking cursor because the system is trying to boot from the Seagate vs. the Corsair Neutron.

I can't tell you how many times I have went into the BIOS and made sure that the the ONLY boot option available is the SSD, I have tried making it the number 1 option with the other hard drive as number 2 etc...etc...I have tried every configuration and no matter what I do it tries to revert back to the Seagate as the number 1 boot option.

Also even when I have the OS booted up on the SSD it runs slowly and gets hung up and applications don't respond. The minute I take the mech HDD out everything runs smoothly again.

Any advice on this problem is greatly appreciated. Full system specs are in my public profile. Thanks.

Thanks in advance.