Take the motherboard out. Check to see if there are any extra standoffs that your new board doesn't need - you could be shorting it out causing it not to start, or try and fail to prevent damage.
It's one of those "oh duh" things, but it's something to check before sending the board off.
I have seen some cases which have raised portions where the motherboard rests on, but they cause problems with some boards which don't always follow spec exactly, or the case doesn't.
Another way of diagnosing - run the motherboard outside of the case. Just set it on a non-conductive surface such as cardboard (not coated with anything) and bare minimum RAM, CPU and see if it runs. Don't put a video card in, and it should give you the error beep code for no video card installed.