Javascript added via drupal_add_js() does not get aggregated
The reason it wasn't aggregating is that someone had every_page set to FALSE and preprocess set to FALSE(as @thedotwrite was saying in comment above) in a lot of  drupal_add_js() calls.  (Some of them were set like this because they really shouldn't have been on every page but there were some that really could be on every page).

Not sure why I didn't notice that before :)