here what I suspect
the os need 2 partitions the boot and the system one, the boot is where windows is , and the system is where are the files like ntldr boot.ini are .. both partition are usally in the same partition C:\ ( I know it's look funny ) . but if you use an old drive with as exemple vista on it , and install 7 on an other drive. the 7 can install the system files in the new drives, but lives the one on the old drive .. now it's look like the bios point to the old system partition .. the boot.ini you look at is in the new system partition, your c:\
when you reset the bios you probably set the old drive as boot device . you may have other posibility , but they are all results of mismatch the boot and the systems files , in too many install .
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