kicksville
Thanks for filing with tech support, Jlien...curious to see what they say when you get through to 'em. I was wrong about one aspect of this little bug, though: it doesn't matter what the lowest note in the entire track is, it's the lowest note currently displayed that exhibits the problem. So my idea for a workaround to insert a C-1 at the very beginning of the track won't work. Inserting a note below the one on which you're trying to edit, then deleting it, works fine. Or, change to the edit, move, or delete tool, and you can bring up the note properties. Such a wee little bug, but it definitely gets old if you're doing a lot of editing below the staff 
Jerry - tried what you suggested, but it doesn't matter where you click on the note, regardless of how far zoomed in (at least on my system). If the note is BOTH below the staff AND the lowest note currently displayed, right-clicking the smart tool will not bring up the note properties dialog,
Shawn - that was such an insightful answer! Very helpful.
And by "insightful" and "helpful," I mean "wow, this guy actually took the time to snark at somebody who was looking for an answer." Nice! 
Are you using the pencil tool (not the selector tool)? This is a very intermittent bug on my machine, sometimes I have no problem clicking on the lowest note on the staff, even if it's on a ledger line. Other times I do. I filed a Cakewalk Problem Report about this, thought it was fixed in X3d, but it's not really completely fixed. There are easy workarounds:
1. Use event inspector
2. Use event list
3. just select the note and call up process menu to do what you need to do on that note
As I said, enlarging the staff view usually does the trick. Make sure you're using the pencil tool!
If you're still having problems, it could also be related to the type of graphics card and/or graphics driver you're using..
Jerry
www.jerrygerber.com