It is the Business Ready Finisher or the L/X finisher? If it is the Business Ready Finisher, you do have to make sure you wait a full 10 seconds before re-inserting the waste container for it to reset the counter.
We have an AltaLink C8055 with the 2/4 hole punch finisher installed. It has a huge waste tray, but literally 1 CM of paper punches in the bottem sends the message out that it needs emptying. It is crazy as it's barely 5% full. We are at a large college so it's constantly needing emptying. Is there no way to configure this to act normally? I have searched every resource. We payed a lot for this device.