Serial FlashLoader

I would recommend filing a Service Request on the Altera support site https://mysupport.altera.com/eservice/ when you encounter an issue such as this. The workaround appears to be setting the Configuration Pins to "Use as Regular I/O" and this will get you past the fitter. Some internal settings are conflicting and this will most likely be addressed in a future service pack.

Make the settings here: Menu Item "Assignments", "Settings", "Device" sections, click on the "Device & Pin Options" Button, Dual-Purpose Pins tab, set all of these pins to "Use as Regular I/O". This will allow the fitter to map the serial loader pins to dclk, ncso, data0, asdo to be the same as the ones connected to the Active Serial configuration device. I have attached an example Verilog implementation of this. This is for Quartus v7.1.