Oh dear... that reminds me of what happened to my system, but a CMOS clear worked since it was only a temporary prodecdure.
What you've done on the other hand though is a permanent change
Its accepted the new BIOS and replaced the old one it seems. Thats probably why CMOS clear isn't working, since its basically going back to the one that doesn't work.
To test it though, take out the BIOS battery this time, and leave it out for about 20 minutes or so (not sure exactly), and then place it back.
Thats all I can suggest
Other than that, I don't know how to replace a BIOS chip, though I know its possible, as most are removable.
What MSI board do you have?