Next time someone has their bonnet open, could you please check whether your lid matches the shape of the box.
On mine the 2 clips nearest the windscreen fit fine but the other 2 clips (forward) miss the box by at least an inch and that area of the lid is straight whereas the box is shaped.
Mine rattles cos only 2 clips work.

I took my lid off when I first had the car and yes it is awkward to get back on and fitted correctly, and like you say it looks like theres something wrong and it wont clip in as it should, but a bit of fiddling and twisting and it will fit as it should. I was only wrong once and thats when I thought I was but wasnt.

2010 Freelander 2 XS Stornaway Grey
2010 Aston DBS Morning Frost
2010 Bentley Continental Brooklands Green

Too right its fiddley. I had to jump my Audi with the FL the other day and tried for good 5 minutes to get the box lid back on and failed. it was -4 and my fingers were getting numb, so i jusst jammed it on as best i could. i should really fix it properly.......

I accidently discovered the easy way to replace the lid. Just place the lid back on top of the box with about a 1/2 inch gap at the back. Then just slide it towards the windscreen. Takes less than 5 seconds (rather than the 1/2 hour it took me to replace it the first time I removed it).

Thanks for replies - me being plonker but now sorted - thanks

i had the same issue few weeks back... ones you get the hang of its okay. designers could have made it easier though.