Yes, there is an issue with the LVPECL I/O assignment in the Quartus® II software when targeting a Stratix® V device.
The Quartus II software will not implement the "n" side of the LVPECL pair in versions 11.0, 11.0SP1 and 11.1.
You can use the LVDS I/O standard instead of the LVPECL I/O standard because LVDS input buffers are used to support LVPECL input operations, but internal termination is not supported for the LVPECL standard.
This issue is fixed in the Quartus II software version 11.1SP1.