I've not heard of an alcohol scanner being used. If I were you I'd simply put the rubbing alcohol in your carry-on along with the syringes and explain it should they ask about it. This won't cause them to pull your checked bags aside for a special inspection. Medical alcohol is routinely brought aboard - lots of diabetics out there.
From what I've heard RCI is not making an issue out of reasonable amounts of soda or bottled water being brought aboard.