One thing I found is that sometimes when you install from USB, the installer assigns sda to the USB instead of your hard drive. Subsequently your partition table is all messed up. You may want to check that. Generally I try to install from the CD to avoid this issue.
When I did install 13.04 (to dual boot with Win8) I had to go into the BIOS settings to change which drive boots first. Note I am trying to get GRUB to manage the boot, not Windows so we're different here.
What I have right now is that if I boot normally I get the GRUB menu which loads Ubuntu fine, but if I select Windows 8 from GRUB it fails to load Windows. If I boot the laptop using the menu button on the side I can select the Windows partition (using the Lenovo's boot order option) and Windows 8 will load fine (bypassing GRUB). So not an ideal situation but it at least works somewhat.
So I can't answer your question directly but hopefully my somewhat similar experiences will help you.
I'd be interested to know how you set Windows to manage the boot process, though.