So what you're saying is, even with the floppy drive and floppy drive cable completely disconnected from the motherboard, the floppy LED still lights up and stays lit?
Edit - I have a vague recollection that some CF adapters "trigger" the floppy LED as a way of indicating activity on the CF card. I only have a very vague idea that this is possible with some of them. Could it be a possibility with yours? Did the issue start the same time as you installed the CF adapter?