Try running chkdsk
to find and repair any errors on the hard drive. I am assuming you are running Vista. If you are using XP, the procedure
is almost the same.
If you are getting to the green bar I doubt it is a boot sector problem.
If by chance you are using XP, you could do a repair installation (using a full XP installation disk) and not mess up the rest of your programs and data. If you are using Vista I would recommend you start backing up your files now.