Description
Due to a problem in the Quartus® II software version 10.0, the Enable input tri-state on active configuration pins in user mode option on the Configuration panel of the Device and Pin Options dialog box is disabled for Cyclone® III, Cyclone® III LS, Cyclone® IV E, Stratix® III, and Stratix® IV devices.
Resolution
To work around this problem, you can enable this option by adding the following assignment to your Quartus II Settings File (.qsf):
set_global_assignment -name TRI_STATE_SPI_PINS ON
This problem is scheduled to be fixed in a future release of the Quartus II software.