DS-5 debugger "run" or "start" option lead HPS to reset

If you used the Qsys system that targeted the Arrow board and used it for your custom board did you remember to change the SDRAM to LPDDR2 and modify the timings? If not then that's probably what's wrong. After you generate the system you should also run the I/O constraints script for the SDRAM controller to make sure the necessary constraints are added for LPDDR2. For information about running the SDRAM constraints you can look at the Uniphy user manual which applies to the HPS memory controller as well.

If you forgot to make those changes in Qsys and your custom board has a different pinout you might need to change the HPS pin muxing options to match your board as well as the pin assignments and constraints in the Quartus project..