Here's what I would do...You've got to figure out if its ransomware/virus/rootkit...etc or something legit in the bios. I would try these troubleshooting steps...
Install virtualbox on the linux side, create a raw disk virtual box...(https://www.virtualbox.org/manual/ch09.html
) Chapter 9.9. Try to boot to windows...you might have to use boot repair to fix the virtualbox to get it to boot. If it boots up with out the warning then most likely windows is fine, which points to the bios. If you see the warning, then windows is toast. Wipe it and start over. If you have files you need to save, put them on a storage device that you don't care that much about, the saved files could be infected...you can clean it all later.
If it is the bios try this...
pull out the hard drive and fire up the machine. If you still get the message when entering the bios, then it's definitely a bios thing. If you get no message, it could still be the bios. I would then do this,
reset your bios to all default settings. . If you saw the message without the drive try booting again. See if you get the message. If you still see it, you could try pulling the CMOS battery (look for how-to's on youtube. It's simple)
If you still see it without your drive...then get rid of the computer.
If you see no message...
Connect a different drive and boot, see if the message appears. If no message, then it's something on the drive, if there is a message, then it's still on the Motherboard somewhere.
If you narrowed it down to the drive. Back up important files on a secure external drive with nothing else on it that could be infected. Again, you can clean these files later.
Put your original drive back in.
Reboot, go back into bios make any appropriate changes to boot to a .usb or cd. Use something like DBAN (http://www.dban.org/
) to wipe the entire drive, and start over with clean installs of everything.
start with a windows install...keep it small like 40-60 gigs. It'll take forever for windows to install and update...you know, leave it for days to finish.
Once it's done. Install your linux using the partitions the way you would normally do...5 minutes later when linux is installed and updated :) create the virtualbox for the raw partition and you're back in business. You won't need to dualboot anymore either, you can just use linux.
And hopefully that annoying message is gone.