There is a known problem when using the PLL Reconfig Controller Intel® FPGA IP with the ALTLVDS Intel® FPGA IP in external PLL mode, in the Quartus® II software version 14.0 when using Arria® V, Cyclone® V, and Stratix® V devices.
After compiling and fitting the design, you might find that the duty cycle for the C1 counter reported in the Timing Analyzer does not match the calculation that is described in the related solution for a user defined data rate.
To work around this, the PLL Reconfiguration Controller must be disconnected from the external PLL IP that is driving the ALTLVDS Intel FPGA IP.
This problem is scheduled to be fixed in a future version of the Intel® Quartus® software.