So, I don't know what exactly how I managed to delete the MBR record on windows partition. But let me explain what I did next, I ran the ubuntu boot repair tool and now Windows is not even listed in my grub loader.

So I went and booted with windows cd and choose repair. Then I ran ubuntu boot repair again via live cd. Here is the log http://paste.ubuntu.com/1426181/. Still no luck.

Looks like osprobe can't detect windows on my /dev/sda2 partition. Any clues ?

Here is how my partitions look like:

Disk /dev/sda: 500.1 GB, 500107862016 bytes
255 heads, 63 sectors/track, 60801 cylinders, total 976773168 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x525400d1

Device Boot      Start         End      Blocks   Id  System
/dev/sda1   *        2048      206847      102400    7  HPFS/NTFS/exFAT
/dev/sda2          206848   509620669   254706911    7  HPFS/NTFS/exFAT
/dev/sda3       509622270   976773119   233575425    5  Extended
/dev/sda5       509622272   957757439   224067584   83  Linux
/dev/sda6       957759488   976773119     9506816   82  Linux swap / Solaris