In the scene where William and his friends first meet the naked Chaucer, there is a part where Chaucer sits down in the grass butt-naked...during this time you can clearly see that he is wearing boxers, then the next clip he is not, then he is wearing them again...
No he isn't. Listen to the commentary on the DVD and they (the director and the actor who played Chaucer (Paul Bettany)) talk about how they used duct tape to hold his 'parts' out of view and he was indeed fully butt-naked throughout the scene