First, while I could be wrong, I'm not sure that it's the Windows protection kicking in because how are you supposed to even access the OS if you're being thrown straight to the BIOS? In my experience with that protection and Windows 7, you are able to boot up until the login screen where the OS will let you know that it thinks something is fishy, and then have you contact Microsoft. If you're being thrown directly into the BIOS, then how would any user know to call Microsoft? And at what phone number? They wouldn't.

However, I don't doubt that you might end up seeing that Windows OS protection thing pop up once you finally reach the login screen because you changed out the motherboard.

Second, I also don't think the code that the motherboard is showing while in the BIOS is important, but I could be wrong (again). Normally, the motherboard either has its own code to let you know you're in the BIOS, or it will show the CPU temperature if the manufacturer has implemented that. On my X79 Asus board it shows a code of "AA" when I'm in Windows, which is just a code to indicate that it has fully booted. Your motherboard's manual says "99" means "Super IO Initialization" ...whatever that means, but if you're in the BIOS and the board is working at that point, then it probably doesn't mean anything other than "you're in the BIOS."

Third, it doesn't sound like the system is even trying to boot to the drive since you're getting thrown directly into the BIOS. If it was failing to boot there should be some type of error message that pops up after the BIOS has gone through its tests, and it would say something along the lines of: "No system disk found".

I believe all BIOSes these days have some sort of way to directly boot to a device straight from inside of them, and I would try that. If you make changes to the BIOS before trying to boot from the device it will likely want to restart the machine, but if you make no changes and just "force boot" from a device, it should try to load it up right from there. Looking at your motherboard's manual, it says there is a boot override option, which sounds exactly what I'm referring to.

Ultimately, the problem may also be that you're trying to use the old install on the disk, since it currently has its own chipset drivers which were meant for another motherboard, so a fresh install may be what needs to be done, but you can also try another SATA port if you want (the ones closest to the RAM are the primary ones according to the manual). Or it may have something to do with UEFI and secure booting, but I'm not familiar with any of that stuff.