I think the problem lies in the fact that Ubuntu cannot access and alter the bootloader in your system. This can be corrected by installing it properly. I found the following answer on the website bleepingcomputer.com
1.Boot from the Live Linux CD.
2.Choose an option that says something like "Try Linux without installing".
After Linux desktop environment (like Gnome or KDE) is finished loading, open a Terminal window.
3.Under Gnome, open Terminal through, Applications menu -> Accessories -> Terminal.
4.In the terminal, type sudo grub.
5.Next type, find /boot/grub/stage1 and press Enter. The output may look like hd0, 6
6.Type root (hd0, 6). Note that we have to use whatever output we get from previous command. If you get hd0, 2, then type root (hd0, 2)
7.Type setup (hd0) (again replace hd0 with the output of the find command) and press Enter. next type quit and press Enter to exit grub.
8.Thats it, Grub bootloader is loaded again in MBR.
9.Restart your computer.
Try this... If it does not word, use BCDEdit... I found the following answer in Microsoft Community
1.Download and install Visual BCD in Windows 7.
2.Then run "Dual-boot Repair" tool - it fixes the BCD in a single or multi boot environment.
3.For installing Ubuntu alongside Windows see this tutorial.You need only a logical partition for Ubuntu installation.