If you upload a file with keywords embedded in the metadata the system uses them by default and does not provide auto-keywords. While this can't be changed you can access the auto-keywords with just a couple clicks of the mouse.
Under the keyword boxes click "Erase All Keywords." Once your embedded keywords are gone click "Refresh Auto Keywords."
That should populate auto-keywords for you.
If you want to use both then I recommend you click the "Paste Keywords" tab in the upper right corner of the keyword box, copy your embedded keywords then follow the steps listed above followed by pasting your original keywords back in. You can delete any duplicates before submitting.
Cheers!
Mat Hayward