Yes, when you use LVPECL on a dedicated clock input on a row I/O bank, the Quartus® II software versions 7.2 SP3 and earlier incorrectly allow you to assign 3.0V and 3.3V I/O standards to output pins in the same bank as the LVPECL clock input.
When you use LVPECL on a dedicated clock input pin located on a row bank in Stratix® III devices, VCCPD must be connected to 2.5V. When VCCPD is connected to 2.5V, the I/O bank can support only output operations for voltages less than or equal to 2.5V.
This issue is scheduled to be fixed in a future release of the Quartus II software.