I do not know if this will solve your problem, but for me the cRIO will only outputs to the compiler or debugs if it has a static ip address. (Windows has a dynamic ip address by default) When using a dynamic ip address, our computers never get past the "Waiting for cRIO to reboot (##s)"
Info on setting up static ip address
You should set your ip address to: 10.XX.YY.ZZ
(XX.YY is team number [123 -> 01.23] ; change ZZ so that no two computers on the network share the same address)