What board are you using? Any chance you can post your rbf? I have been trying to get the FPGA to load from u-boot for like a month. I will change my script to match yours exactly.
As far as the problem you are having now. At one point I was trying to write to /dev/mem to a GPIO and I had the kernel reboot on me. Still have no idea what was causing it. My best guess is that there is some errant FPGA2HPS interrupt, although whether it is caused by your hardware design or something in the kernel, I have no idea. I would begin by investigating irqs in the CycloneV manual and see if there is one that might cause a kernel reboot and what would trigger it.