Kelly, tough spot you're in. Unfortunately, I have to agree with the posters who have thus far suggested there was something shady about your set-up. I won't rehash all their points, but I assume you're playing Yahoo? And you literally posted a Commisioner's Note, correct, not a message on the league's message board? In my Yahoo league, you don't even see the option to read the commisioner's note from my main team page -- I have to click on "All League Tools" to see the option to see the Commish's note. I'm sure there are people in my league who are knowledgable fantasy players but not so Yahoo savvy and may not realize that note is there. Just one more point that makes me think your disclosure wasn't much of one . . . although I have to admit I can't remember if "Commisioner's Note" was a main page option predraft.
Good luck. Friends above all else, so you and the guy in second might have to suck it up and toss the pot back.