Due to an issue in the Quartus® II software, the phase shift that you set in the Altera_PLL megafunction may not be your desired value.
This only occurs with certain multiply and divide factors. When this does occur, the actual phase shift will be shown as 0ps in the megafunction.
To workaround this issue, you can manually change the "phase_shift" value in the generated <user_define_ip_name>_0002.v file.
Find the .phase_shift<clock output number>("0 ps") parameter and change the value to your desired phase shift value.
For example, if you wish to set a 1200ps phase shift value on clock output 0 (C0), you would change the parameter as shown below:
.phase_shift0("0 ps"), // original value
.phase_shift0("1200 ps"), // modified value
This is scheduled to be fixed in a future version of the Quartus II software.