Interesting that you found this out - which dean notified you and how'd he end up getting a look at your letter? Subtle biases can wreak havoc in things like recommendations, as any Psych 101 student can tell you. Remember that it's late in the game and, though I can't give you definitive LoR advice, if I were in your shoes I'd ask myself:
How will this letter seem to an AdComm who has 10 minutes to read my application and 45 seconds to skim this letter? If the answer is anything less than "seriously worrisome and off-putting" I wouldn't worry, especially with so many other soft factors for him or her to read about.