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Sorry if the subject is already answered but I can't find the solution.

I have a clean install of Windows 7 and I installed ubuntu 12.04 as a second OS. I manually did this partitioning using gparted

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The boot loader of Windows is in /dev/sda1 and the Ubuntu one is in /dev/sda3. When I installed Ubuntu and first booted, the PC just didn't boot at all, so I booted from Ubuntu live CD and repaired GRUB.

After that:

When the ext4 Filesystem is flagged: boot:

Ubuntu starts with the boot loader but works fine only if I choose Ubuntu.

If I choose Windows then the problem comes;

No mouse present before pressing power button on, leads to the starting of windows (chosen from the loader) but lacking of mouse.

If I boot like this and then plug the mouse (I've tried a wired Microsoft usb mouse and a Logitech wireless with receiver), it's just not detected and all the updates I can do for my motherboard require clicking a mousebutton, keyboard doesn't work for the final proceed command(even for installing the drivers of the motherboard using the CD).

With mouse present(plugged in) before pressing power button on, leads to the boot loader and if I choose Windows I end up watching a purple screen and no response, after reading a

FATAL ERROR : One or more table pointers are invalid. Modification could be unsafe. Press any key to continue booting.

When the NTFS Filesystem is flagged: boot :

Windows start but they boot alone without boot loader, not giving me the choice to pick the OS. Furthermore Windows before start loading, tell me about the same (mentioned above):

FATAL ERROR : One or more table pointers are invalid. Modification could be unsafe. Press any key to continue booting

After that Windows start normally.

So, what should I do to have a nice boot loader(Windows or GRUB) working?

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try boot-repair disk. –  Avinash Raj Nov 16 '13 at 15:37

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