Jungle Rollers: For the three extra boxes, you will need the green gem which can be collected in The Lost City (if you finish the level smashing all the boxes without losing a life). To do this, in the 4th cubby hole on The Lost City, just on the striped box at the end and press the X button off it to get an extra boost and this will activate an ! box which will create the box further on which I had trouble with. Once you have the green gem, go to Jungle Rollers and, when you find the green gem, jump on it and then jump on the arrow box and then onto the green gems and the boxes are there!

The Great Gate: You will need the yellow gem which can be obtained by smashing all the boxes (without losing a life) on the level The Lab. Then at the end of The Great Gate, if you jump on the yellow gems over the finish portal, you will be taken to an extra part of the level.

Upstream: For this box, you will need the gold gem from finishing the level The Generator Room, again having smashed all the boxes without losing a life. Then, under one of the moss logs are the gems. Directly under the log, out of sight, is a box with an extra life in.

Rolling Stones: For these you will need the blue gem which can be obtained from the level Toxic Waste in the same way as the others. Then, about halfway through the level, you will find the gem floating next to the pillar you are stood on. Jump on it and it will take you down into an extra part of the level.

Native Fortress: When you come across an arrow box, jump over the fence behind you and run along to find the boxes there. Get out when you find the next lower section of the fence, then run back and smash the arrow box.

Hope this helps!