This likely because the majority of the airflow is now bypassing the carbon pile.
My original design had airflow holes full diameter and lacked the upper baffle. Your change effectively duplicated that design. The problem was the airflow largely bypassed the carbon pile since it is difficult, if not impossible, to get the space below the HEPA filter completely filled with carbon pellets. Hence the addition of a solid baffle.
One way to test the effectiveness of the carbon pile is to inject inspection smoke into the air-stream and observe how much of that makes its way through the filter. For this test remove the HEPA filter so that it is not removing the test smoke. Amazon has a number of products that generate detection smoke. Search for "leak detection smoke".
As it turns out the carbon pile provides a significant portion of the drag on the airflow. That is why it is necessary to use a fan that can overcome this drag (High Static Pressure Fan). They tend to be a little noisier because of the airflow cavitation around the fan blades.