The Quartus® II software may issue this warning when trying to merge PLLs for the ALTLVDS_RX megafunction and the ALTLVDS_TX megafunction with DPA enabled, even though the clock frequencies are the same. This affects Stratix® III and Stratix IV devices.
For example: the PLL post scale divider (k) has a limit range of 1, 2 and 4. The best VCO frequency for an ALTLVDS megafunction instance without DPA enabled is ~600MHz, however 600MHz cannot be used to generate a 200MHz DPA frequency because 3 is not a valid divider value.
When using the ALTLVDS megafunction without the external PLL option, you do not have any control over the PLL settings in the Quartus II software. As a work around, you can use the ALTLVDS megafunction in the external PLL mode. This allows you control the PLL values and manually assign the PLL clock outputs to the ALTLVDS_RX megafunction and ALTLVDS_TX megafunction instances in your design, thus allowing PLL sharing.
For further information on using ALTLVDS megafunction in external PLL mode refer to the ALTLVDS Megafunction User Guide (PDF).