After you have installed Ubuntu and the computer is rebooting, you have to remove the USB because the computer will still boot the USB before the harddriver, as you specified in the BIOS settings.

Manual partitioning

Consider that this list is long because it guides you closely and was intended to be very comprehensive.

I think this list of steps should fix your problem, but only run it if you can re-install Windows (in case anything goes wrong or you care about having it):

1. Backup the data on Windows' you care about, i.e. user files, applications, etc.
2. Defragment your hard-disk. This can be done from Windows.
   Contrary to intuition, files don't stack up in order in a hard-disk. They can be represented by spread out papers in a box. When you create a new partition you are chopping this box into two pieces: the first being your Windows partition and the second your Linux partition. If your Windows files are stacked up in the Windows piece of the box, you will lose no data the moment you divide your disk; otherwise you will. To stack the Windows files as required - at the beginning of the partition - you defragment the disk.
3. Boot from the USB and "Try" Ubuntu.
4. Partition your system with gparted.
   There are plenty of guides on the subject already which are easily findable. The idea here is that after defragmenting your disk you will be able to shrink your windows partition manually to a desired size, and use all the rest for Ubuntu.
5. Install Ubuntu and when prompted to select the installation type, select manual; there you will use the partitions you made on step 3.
   Make sure that in step 3 you create a primary partition for GRUB, and that in this step you will let Ubuntu install GRUB in such partition.

By installing Ubuntu this way, you are assured that Ubuntu has available as much space as there is available.

Maybe you already did that, but be sure to rename all isolinux* file to syslinux* on the pendrive, as explained in the Unetbootin section of this guide. One time I had a similar problem and I was missing this part.