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Is the exposed pad of the Cyclone III connected to ground?
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I also thought about this point, it's explicitely shown in the schematic. I wonder, if the pin is also known to be soldered correctly?
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at beginning system connects only 3.3V bus, when it is done CONF_DONE looks like in attachment, then 3.3V is off, and then all supplies are on togheter
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I'm not sure, what you are describing here. Is it about a irregular power-up sequence?
According to the hardware manual, schottky diode should be used as AS clamp diodes, I assume that the LED symbols have been used by mistake.
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