Description
Yes, the alignment pattern is set correctly when using the ALT2GXB Megawizard™ in Quartus® II Software Version 9.1 SP2 in Stratix® II GX devices. However when you set the alignment pattern to 20 bits in length in the ALT2GXB Megawizard, re-opening will show an alignment pattern length of 10 bits.
This does not affect the fitter results and hence the Stratix II GX device works as expected with a 20 bit alignment pattern.
This will be updated in a future version of Quartus II.