Due to a problem in the Quartus® II software version 14.0, Qsys incorrectly restricts the minimum frequency of HPS User Clocks to the frequency of the external reference clock (OSC1/2).
To work around this problem manually edit the PLL settings for the user clocks in the <BSP>/generated/pll_config.h file before running make to build the Software pre loader.
Please see the Preloader Clocking Customization Page on www.Rocketboards.org for information on manually editing pll_config.h
This problem has been resolved for the next release of the Quartus II Software