If you are using NCSim to simulate the Altera_PLL megafunction, some of the output clocks may be stuck low.
There are two workarounds for this issue:
1. To instantiate Altera_PLL, check "Enable physical output parameters" in the megafunction, and set the parameters accordingly to get the clocks you want.
2. Enable the macro SIM_USE_ICD_PLL_RECONFIG_MODEL to use the physical simulation model as shown below for Cyclone® V devices. You will need to edit the commands below when targeting Arria® V or Stratix® V devices.
ncvlog -DEFINE SIM_USE_ICD_PLL_RECONFIG_MODEL=TRUE "/eda/sim_lib/cadence/cyclonev_atoms_ncrypt.v" -work cyclonev_ver
This issue is scheduled to be fixed in a future release of the Quartus® II software.