boot - Windows installer creates system partition on another drive

I have a Fujitsu Lifebook U772 which has a 40GB SSD drive and a 300GB HDD.

I decided to reinstall Windows on it. When the installer came to the step to select the installation drive I selected the HDD.

Then the computer didn't boot. I went to try and reinstall Windows when I saw it: The install had created the System partition (with the bootloader) on the SSD.

Now, for some reason the computer doesn't detect the SSD as a boot device.

I already tried creating the System partition manually and making the SSD an ext3 partition (which the installer deleted and created a system one).

How can I make the installer force the system partition on the HDD?