Hi, I would "trust" the pump. The boxes will be the same pictures for every model and someone probably forgot to change all the infomation. The pump should have a more accurate flow rate, although they tend to be ball park figures, because each model has its own stickers.
Edit, after a quick look on their site I'm not sure I was right as their descriptions on the pump all say 6 watts 1000 lph. The boxes state the same info on the sides as well so it wasn't a simple cockup. Their larger 6000 lph model is 20 watts which is a big increase so your probably does only push 1000 lph. You should be able to tell if you run it in a bucket of water because 4000 lph makes quite a push.