i dont know if it will be any help but i got this problem a while back when reinstalling windows nt onto a fat partition i made using linux fdisk. When it happened i had a lot of games on my hard disk and did not feel like losing them all so i just shut down and rebooted. When i restarted all my data was there and i have been using the same partition ever since. In essence i ignored the problem hoping it would go away, and it did, though i would not advise this. What you should do is remove windows and devote your entire hard drive to linux
Bad sectors are not really much to worry about. I have a couple of old hard disks which are riddled with them. windows marks them as bad and so will not use them and they should cause you no trouble other than the small amount of space you will lose form not being able to use them. You may however lose the data thats on them, but there are programs (scandisk) which attempt to recover it.