Hi Sean,
I'd be wary of inferring too much from one week's worth of results. Depending on the site, a 3% variation could just be weekly fluctuations.
A few things might help shed some light on the situation:
When did you make the changes? It's possible that you can rule out your changes as the cause of the differences by figuring out if the search engines have indexed them yet.
I'd take a look at Google Analytics in depth and see if there's any kind of weekly/month variance across at least a year of data. Maybe the first week of the month gets more traffic historically - unfortunately I've found SEOmoz doesn't provide data back far enough to catch this kind of thing.
I'd also use GA to compare month-to-month traffic and see if there are any keywords or phrases that are receiving less traffic for each portion of the month.
Have you seen any ranking changes? There's a slight difference in URLs receiving entrances compared to last week. These might account for a drop off if a page has stopped ranking for a specific phrase. I'd be surprised if you lost traffic by removing those duplicates you mentioned, as it's less common for duplicate pages to rank twice for the same result, or for them to rank differently for different results.
Again, it could easily just be normal variation, but the above things are where I would start.