Sometimes what we call your boot record gets screwed up.
Thankfully You have what is called a Master boot record, a sort of back up if you like of the windows booting sequence. when you boot from say the option in windows by pressing the F8 option, and selecting boot from last know good settings windows does a check and compares the master boot record to the boot setup of windows. any corruption to the boot record of windows is corrected by copying the information stored in the Master boot record of the Hard drive.
Even if you boot into safe mode windows will do a check of windows boot record and compare it to the master boot record.