Fixing misaligned Windows partition without affecting Ubuntu

I have dual boot setup with my partitions set up like so:

• /dev/sda1 - DellUtility (FAT)


• /dev/sda2 - RECOVERY (NTFS)


• /dev/sda3 - OS (Windows 7 NTFS)


• /dev/sda4 - Extended
  
  
  
  • /dev/sda5 - swap
  
  
  • /dev/sda6 - ext4 (Ubuntu OS)
  
  
  • /dev/sda7 - ext4 (Ubuntu home)
  
  

I used Clonezilla to clone my hard drive and clearly screwed up something since now Ubuntu's Disk Utility reports that my partitions are misaligned. I can boot and use Ubuntu with no problems but Windows refuses to boot and shows a Windows Boot Manager error screen with status code 0xc000000e:

I have a Windows installation disc but I'm worried that "Repairing my computer" could affect either grub or my Ubuntu partition. What's the best way to recover?

Answer

I followed the instructions on the error screen. That is, I inserted my OS disk then ran "Repair your computer". It worked like a charm. I can boot Windows and Ubuntu with no issues.