I'm having suddenly increasing issues with this type of behavior. The two approaches that have been successful for me is to either fill the cage with nest boxes so she has no option but to use one of them, or to bring the doe inside in a medium-sized dog kennel filled with hay on the night she's due (again, leaving her no choice and keeping the babies from scattering. Once she's had the babies, I move them to a box with the bedding they've been born in and replace her and the box back into her cage.
If you have baby saver wire around the bottom of the cage, putting plastic mats down might help, but the kits may still end up crawling all over the wire and being scattered if the doe doesn't make a really snug nest. However, if you can catch the babies in the out-of-the-box nest just after they're born, you should be able to transfer them into the nest box with their nesting material. Once they're born, the doe doesn't seem to mind where she has to go to feed them.
I am honestly mystified at what's going on. The only time I've ever had this problem before is when mice were getting into the nest boxes while they were in storage, and the does did not like the mouse smell at all (can't say I blame them!). Of course I solved that problem, but this spring, it's old does, new does, does of different breeds, old nest boxes, new nest boxes, metal nest boxes with wood floors, wood boxes, wood boxes with wire mesh floors... but a majority of my bred does are rejecting the nest boxes. I am just about pulling my hair out dealing with it!
