Half of ram usable, and low transfer speeds since upgrading

I recently upgraded my computer by replacing my motherboard, case, and power supply. At first I figured everything was done right, and it took a while before I realized that windows finds 12GB of ram, 5.99GB usable. Besides that, I also find that my transfer speeds by usb are incredibly slow, hitting a max of 5.7MB/sec, and normally sitting around 3.8.
I cant imagine what went wrong, except for fearing the worst; a bent pin on the cpu. I don't actually have any thermal paste, and cant remove/reseat it, so does anyone have any suggestions that might be causing these issues?

You sure you installed Windows 7 64-Bit, and not 32-Bit?

I didn't reinstall, I used the same hard drive I'd been running for the last year and a half. And yes, I'm sure its 64 bit. Doesn't 32 bit only use 4GB anyway?

first--a bent pin on the CPU would keep the machine from booting

second--if your listed specs are correct--mixing different Ram speeds will cause your mobo to run all the ram at the slower speed.

third--check BIOS to see how much RAM the MOBO sees.

fourth--USB problem 'may' be related to the mixed RAM

I had seen a post not long ago on a different website where a bent pin caused the same problem with the ram that I have, which is why I am worried.
As for the mobo, it also sees the 12 gb. I'm fine with running at the slower speed, My problem is with the fact that it can only use half of it.
I already tried removing the ram, and even with just the 2 corsair sticks, my computer said 8GB (3.99 usable)
Besides that, this ram in this setup worked perfectly with the old stuff, but I guess the different motherboards might cause issues...

fifth--read documentation that came with MOBO

On what exactly? I already read the ram installation part... It didn't really say much besides informing of where to install them for dual channel modes, and I took care to follow the first time.

If you had a bent pin on the MB it more then likely would not boot.

So what do I do to fix this?

Does your BIOS have an option for enabling memory mapping, or something to that affect?