(The following is an example of description in pll_config.h)

#define CONFIG_HPS_CLK_OSC1_HZ (25000000) ←Duplicate (1)
#define CONFIG_HPS_CLK_OSC2_HZ (25000000) ←Duplicate (2)
#define CONFIG_HPS_CLK_F2S_SDR_REF_HZ (0) ←Duplicate (3)
#define CONFIG_HPS_CLK_F2S_PER_REF_HZ (0) ←Duplicate (4)
#define CONFIG_HPS_CLK_MAINVCO_HZ (1600000000) ←Duplicate (5)
#define CONFIG_HPS_CLK_PERVCO_HZ (1000000000) ←Duplicate (6)
#define CONFIG_HPS_CLK_SDRVCO_HZ (800000000)
#define CONFIG_HPS_CLK_OSC1_HZ (25000000) ←Duplicate (1)
#define CONFIG_HPS_CLK_OSC2_HZ (25000000) ←Duplicate (2)
#define CONFIG_HPS_CLK_F2S_SDR_REF_HZ (0) ←Duplicate (3)
#define CONFIG_HPS_CLK_F2S_PER_REF_HZ (0) ←Duplicate (4)
#define CONFIG_HPS_CLK_MAINVCO_HZ (1600000000) ←Duplicate (5)
#define CONFIG_HPS_CLK_PERVCO_HZ (1000000000) ←Duplicate (6)
#define CONFIG_HPS_CLK_EMAC0_HZ (250000000)
#define CONFIG_HPS_CLK_EMAC1_HZ (250000000)

Tools: Quartus II
Tool version: 14.0
Device: Cyclone V


Yes, it is a bug in Quartus II v14.0. (Common to Windows and Linux versions)
However, since the same macro name contains the same value, there is no possibility that this event will affect the operation.
This will be fixed in a future version of the tool.