Due to a problem in the Quartus® II software version in 14.0, the configuration of the variable CONFIG_HPS_PERPLLGRP_PERNANDSDMMCCLK_CNT defined in the pll_config.h can stop the HPS from booting when both the NAND and SD/MMC controller are disabled in the Qsys HPS GUI.
To work around this problem, either enable at least one controller if possible, or modify the value #define CONFIG_HPS_PERPLLGRP_PERNANDSDMMCCLK_CNT (4) by hand.
This problem is scheduled to be fixed in a future release of the Quartus II software