If Ubuntu is the second one installed, usually all help is when installing on one HDD, considering that you have installed it on separate HDD's then I don't think it matters.
Part of the problem could be that you are using a separate HDD and the OS's aren't picking it up. So my advice will be all trial and error but hopefully you will get it sorted with my help.
Now the usual way when Ubuntu is installed second over the top of the second the grub replaces the MBR record so you use grub and do the following
To enter the GRUB configuration mode, type in
sudo grub (from command-line and press Enter.) Then type in the following commands in sequence:
The above should work in grub boot commandline - else use live CD and just run from CD and use the terminal.
In your case, you would want to make some changes to this as this setup assumes that you are on the same HDD. Change all "hd0" to "hd1".
So it will look like this:
What you are doing is getting grub to pick up the Windows 7 installation and set it up in the grub.
Alternatively you will need to do a reverse with the Windows 7 but alter the MBR information within Windows 7 by adding an additional line to the boot loader to get it to boot the Ubuntu.
Windows 7 bootloader has been made more complicated and you need to use
bcdedit to modify it. Unfortunately, adding with it could prove to be a big hassle their is an alternative way which is using a program called EasyBCD which will make altering the Windows 7 boot loader easy.
In theory, it should work just remember it is on a separate HDD but from what I have read that shouldn't be a problem.
Check Boot Linux using Windows 7 boot loader for more information on Windows 7 bootloader.
If you want to do it both ways that is entirely up to you but give those 2 options a go and see what happens after that.
Hopefully this will give you some direction as to what might be going wrong with your current situation if it doesn't fix it.