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The problem is solved now.
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Great!
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It was very unclear how Altera called different power pins. I had used an altera Max II before and the unmarked power pin in the Pin Layout represents a 3.3 V. But in this case when i printed out a copy of the pin layout from Quartus the unmarked power pin represents VCCP/VCCR/VCCT. I thought that was meant for 3.3 V for the chip main power supply. So after checking the pin names from Quartus Pin Assignments, there it shows me to be VCCD_PLL, which is meant to be connected to 1.2 V and not 3.3 V. Therefore fixed my problem, I also added decoupling caps to make sure that my power supplies have monotonic ramps. Everything works as its suppose to now. I hope this help any potential users of the Cyclone 3, to be careful about power pins. Altera documentation is horrible at their nomenclatures.
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I haven't seen any problem with their pin assignments documentation. For example, the Cyclone III handbook page:
http://www.altera.com/literature/lit-cyc3.jsp Has a link at the top to the "Pin Connections" guidelines
http://www.altera.com/literature/lit-dpcg.jsp and the "Device Pinouts"
http://www.altera.com/literature/lit-dp.jsp?category=cyc%203&showspreadsheet=y These two documents have everything you need regarding power pins.
Cheers,
Dave
Honored Contributor
