Are you sure that you don't confuse the boot partition on the CF card with the system partition on the HDF? You have two harddrives connected to the virtual Amiga: the HDF and the CF. The HDF contains one partition called System and the CF contains three partitions. So you should see four harddrive icons on the desktop. If you called the first partition on the CF card System, too, then it's easy to confuse it with the HDF partition. You should call it differently.
Note that bootable or not does not depend on the files contained on a partition. AmigaDOS will even boot from an empty partition. To make a partition bootable you need to activate the "Bootable" checkbox in HDToolbox.
It's easy to test if the CF card can boot up your Amiga: just remove the HDF from WinUAE and let the CF card alone. If WinUAE starts with this config, then your Amiga should do, too.