removing "press any key to continue"?

Well, that should have fixed it. Does it still ask to press a key to continue?

I have never had that problem. Might have been because of the mix of ATA drive and IDE drive. I'm just not sure.
Sorry you had problems.


Is it working right now?

I have never had a need to work with ATA hardrives other than a replacement.
Mixing ATA with the IDE is something I am unfamiliar.

The problem is probably something simple but I am at a loss.

Having to run system repair to replace the BOOT MGR didn't strike me as odd, but that not fixing the problem does. Disconnect the second drive and try setting the System Reserved partition as active and run startup repair if needed. See if that solves the issue, then try reattaching the second harddisk. If not, hopefully Greg will know what to do, or I can ask others for more help.

The 100mb System Reserved partition should remain Active. Mark Partition Active and run Startup Repair - Run 3 Separate Times until Win7 starts with System Active flags on 100mb as it was before.

I would also move the paging file off of the WD data drive as shown in the tutorial I linked before. If that fails then I'd want to wipe the WD to see if code in the boot sector is interfering.

Make sure Win7 HD remains set HD to boot first in BIOS setup.

According to the manual for your motherboard you have 4 SATA ports and 1 IDE.> http://www.msi.com/product/mb/P965-N...l#/?div=Manual

The two harddrives should be plugged into 2 of the SATA ports.

These are pictures (Snips) of your motherboard manual.
You do not want to plug one of the harddrives into the JMicron port.

Just use the 4 ICH8 ports as circled in yellow. They marked #1 in the manual already.

That is the next thing I would check that the JMicron port does not have a hard drive plugged into it.

It appears from the screen shot you posted that the JMicron port does have one of the hard drives plugged into it.
That is why you are being prompted.

Bios is asking "are you sure you want to boot that device?"

Plug both hard drives into the ICH 8 ports and the prompt will be gone.
Wish I would have caught that earlier.
I had a feeling it was something simple.