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my MSEL[2..0] is 010, and i connect it directly to 3.3V ( VCCIO) .
and i check my .sch for hundred times and it's the same as ALTERA instructions.
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Strictly spoken, Altera suggest to pinstrap MSEL to VCCA for '1' in
all Cyclone III documents. The suggestion repeats about 30(!) times in the device handbook.
So far about checking hundred times. If I remember right, the device handbook explains, that there's a risk to latch an invalid MSEL configuration, when VCCA is powered before VCCIO with your kind of MSEL connection. You may check your power supply design, if this can happen. In those cases, where VCCA is derived from VCCIO by a LDO, it can't happen. Apart from this special point, I don't see a particular explanation for the observed behaviour, provided all configurations pins are wired as they should.
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