Stratix V transceiver buffers have several circuits to condition the signal before it is transmitted. These include programmable output voltage (Vod) controls and a 3 tap programmable pre-emphasis (2 taps with GT channels). Certain combinations of these programmable settings are deemed illegal by Altera because they result in the output buffer being over or under-driven, or the expected buffer behavior cannot be guaranteed across PVT. The Quartus fitter knows these illegal settings and will flag an error if the transceiver IP is configured as such. The transceiver toolkit's auto-sweep function also knows which settings are illegal and will not check those settings. However, the toolkit's manual mode and the transceiver dynamic reconfiguration IP does not check for the legality of the PMA settings. This is so users can access the entire setting space for investigation or research purposes. Altera does not support the use of the illegal settings for production as Altera cannot guarantee output buffer performance.
The Stratix V PMA Setting Check spreadsheet can be useful when using the toolkit or reconfiguration IP to manually set the Vod or pre-emphasis. The GX channel spreadsheet can be found here: