No, what I meant was did you change anything in the room? Move any furniture, subs or speakers? Bump the gain pot on the back of your sub? Open a door that was previously closed or vice versa? That can have an effect, but probably not as drastic as what you describe. It might just be a weird anomaly. I think it would be a good idea to run Audyssey again, keeping in mind what I said about following the pattern closely and make sure the top of the mic is at ear level.
Let us know what happens when you get the time, and if you have anymore questions just bump this thread and I'll eventually see it.