Yes. This is a known issue in Quartus® II 5.1sp1 and earlier versions of software. When ALT2GXB is configured in “Transmitter Only” mode with a Stratix® II GX device, the MegaWizard assigns incorrect PLL bandwidth settings to the CMU PLL. This issue is addressed in Quartus II 6.0 and later versions of the software.
For designs that use ALT2GXB instance created in “Transmitter Only” mode, the user must upgrade to Quartus II 6.0 or a later version and re-generate the ALT2GXB MegaWizard instance. The new design, after compilation, will have correct CMU PLL bandwidth settings.