Thank you again for all the suggestions/feedback. As I'm sure you can tell this isn't an easy situation for anyone involved, and without having all the necessary details it looks like there's quite a range of possibilities as to why this happened. While I won't rule anything out, since this is a very good friend of mine (in addition to being a roommate), I'm still inclined to take his word and give him the benefit of the doubt as much as possible. I don't think he had any reason to not come clean about what he was told by his bank. But that's not to say there aren't historical financial issues I'm not aware of, that based on some of the previous posts, could have been the cause of these check troubles.
Thanks again for your responses and wading through my limited bank-jargon.