I have seen it before and some times just rewriting partition table with fdisk or fixparts fixes it. As long as there is some sort of corruption in partition table you will have issues. Many tools that try to use partition table see corruption and then do not work.
Extended partition linking to another extended partition
Your partition table is slightly messed up. But it should be easy to fix. Boot into Ubuntu with Supergrub
http://www.supergrubdisk.org/
sudo fdisk /dev/sda
Press "w". That rewrites the partition table. Reboot (using Supergrub) so that the changes take effect.
If Supergrub gets you into your install then you should be able to reinstall grub2's boot loader to the MBR with this:
sudo grub-install /dev/sda
Also fixparts fixs many partition table issues.
Fixparts - Repair broken partition tables (not overlapping issues) & delete Stray gpt data from MBR drives
http://ubuntuforums.org/showthread.php?t=1705325
http://www.rodsbooks.com/fixparts/
First backup partition table, use your drive for sdX or sda, sdb etc.
sudo sfdisk -d /dev/sdX > parts.txt
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