Some of you have experienced problems when using the Nios-II/e Gen 2 processor. If you have problems connecting to the FPGA and downloading the software to the Nios-II system the solution is to change the cpu type to a Nios-II/e classic in the Qsys builder. Remember to reconnect all interfaces including, for the relevant devices, the interrupt priority and associated priority level.
The Gen 2 processor was first available in version 14.0 of Quartus, but maybe still as a beta-version. If you are using Quartus 15.0 it should work fine.