Yes, this is the most likely reason of the failure, when you flash the BIOS it will be set the the default values. If the SATA mode changes windows will not be able to read the contents of the drive correctly to load its files and will bugcheck early in the boot process. Most of the time you will want AHCI mode but you need to use the mode that was in use when windows was installed. generally this is not a big issue, change reboot you should be up and running within the next two boots (try AHCI advanced host controler interface first)
there can be other causes: default boot drive might need to be selected, boot priority might need to be selected
all of these settings can change when you update your BIOS or restore default settings.
Y0GI :
Check your HDD SATA mode in the BIOS. Choices should be IDE, AHCI or RAID. Whichever one it is on make note and try the other 2.
Yogi