Try and take the rubber gasket off, and then put the lid back on. If that works, then you have a problem with the gasket. It seemed the other day i had this problem, and i flipped the gasket the other way and i could get it to clip in.
I put the gasket on the "male" part, then close the box. I also have found the gasket flip works. If I put the gasket in the female part first, I have a hard time closing it.