Okay here is my take on the process, first BIOS does not interact with Windows at all. BIOS checks all the hardware then hands off to the MBR/ Botostrap to do it's job, again BEFORE anything about Windows. Second it can't really be 'bootstrap' or MBR as those are dealing with the Sector and Partion reads of what the files system is and what is set to boot from; again nothing for Windows YET to be involved with.
When you get the "prompt me to manually start Windows or run its repair program" this is a condition of the Windows OS loading its specific files (not bootstrap, as bootstrap would be to see if there is a OS to load and then to hand off to the proper drive /OS to load) to create the enviroment it determines there was a 'bad shutdown' or 'improper shut down' so files arent' properly set to say 'closed' status or other factors. This usually is Windows trying to be protective. Since you keep getting this inclusive to Safe Mode leads to the probability Windows itself needs to be repaired (boot off the DVD and force it to do so) OR the HardDrive has failure errors.
To test the latter, can you open a CMD prompt and run chkdsk /f (will take a long time) and see what the results are. Then do a sfc / scannow , both will require reboots afterwords, and lets see if they come up with any problems.