JTAG Configuration on EP3C120F780 program loss

With VCCIO of 2.5 V, you can use basically the same power supply for VCCA. Sufficient bypassing for all supply pins should be achieved however. You may want to provide additional filter ferrrites for PLL supply pins, but I think, it's not necessary for Cyclone III in most cases.

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It is so sensitive that i had to re-program it everytime.

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In which situations do you observe configuration loss? Are aware of the volatile character of the SRAM configuration? You need a non-volatile memory to keep the configuration permanently. If the configuration gets lost during operation, you are possibly missing required pull-up or pull-down resistors for configuration and JTAG pins, or have an unstable power supply.