There is a bug in Quartus® II software version 9.0 SP2 and previous versions which affects the "ensure glitch-free switchover implementation" in the Cyclone® III device altclkcntrl megafunction. If you select this option, close the megawizard, then later open the altclkcntrl instantiation, you will see the "ensure glitch-free switchover implementation" is not selected. Due to this bug, the altclkcntrl design files created by the MegaWizard™ Plug In Manger will not enable the glitch-free implementation feature.
This problem can be fixed by installing the following patch for Quartus II software version 9.0 SP2. You will need to open your altclkcntrl megafunction instantiation and enable the "ensure glitch-free switchover implementation" option and recompile your project after you have installed the patch.
- Quartus II software version 9.0 SP2 Windows Patch 2.54
- Readme file for Quartus II software version 9.0 SP2 Windows Patch 2.54
- Quartus II software version 9.0 SP2 Linux Patch 2.54
- Readme file for Quartus II software version 9.0 SP2 Linux Patch 2.54
This issue is fixed in Quartus II software version 9.1.