The Quartus® II software versions 8.1 and 9.0 incorrectly disable Parallel OCT on the negative pin of a differential input. This problem occurs when using differential IO standards SSTL or HSTL even with Parallel OCT enabled.
This problem affects only Stratix® III and Stratix IV devices.
To fix this problem in the Quartus II software version 8.1 or 9.0, download and install one of the following patches:
Quartus II 8.1 Patch 0.55 for PC
Quartus II 8.1 Patch 0.55 for PC readme.txt
Quartus II 8.1 Patch 0.55 for Linux
Quartus II 8.1 Patch 0.55 for Linux readme.txt
Quartus II 9.0 Patch 0.03 for PC
Quartus II 9.0 Patch 0.03 for PC readme.txt
Quartus II 9.0 Patch 0.03 for Linux
Quartus II 9.0 Patch 0.03 for Linux readme.txt
This problem is scheduled to be fixed in a future version of the Quartus II software.