Download Bitstream to Cyclone V by using the FPGA manager

Maybe your RBF file is not correct or otherwise not being written to the data port correctly. If the fpga doesn't see the sync words then it will get stuck in 0xB01 forever. The newer kernels, 3.9 i think, have an fpga manager driver. So all you need is to copy the RBF to /dev/fpga0. I haven't actually tried this though. Newer kernels also don't take the fpga bridges out of reset so you will need to do that after programming the fpga. There is some sysfs mechanism for this as well.