Nah, its not the HDD. I got that the day the HDD bundle was released.
I went and removed the FFXI stuff off of the HDD then tried again, no dice. Going to the browser showed no disc at all if I had the HDLoader disc in there for boot-up.
It was recognized, however, by inserting the disc while the browser was open. Since that first time, the HDLoader disc works fine straight from boot-up.
Thanks for the suggestions, everyone.
It is interesting to note that software meant to make your gaming faster takes well over a minute to boot up itself... I don't suppose there's a key combination that shoots you back to the HDLoader interface without rebooting after you have already started a game, is there?