I know this is ridiculously old -- but I'm back trying to work a bunch of emails that I've forwarded into GTDN, and I'm still having the problem.
I can delete all the content in the note section, and if I move away from the item (on to another one), it is still there. It's like I need some sort of Save button for edits in the Notes section.
Now, if I delete everything, then type a single character (like a space), it keeps the single character. Then, if I come back and delete the single character, it finally clears out the notes section.
I suppose I could just have single spaces in the notes sections of my tasks ... but I thought it might be a bug you'd want to know about. The four-step process to clear them out (delete all, type space, move away, come back and delete space) is a little annoying, but not horribly so.