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The other supplies are turned on by a micocontroller.
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If the supplies are used by the Cyclone, then make sure the power-on sequence meets the requirement of the FPGA power-on-reset. If it does not, then you may have to assert nCONFIG low until all the supplies are valid.
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Good idea to check for clock, you nailed it! I find no clock on my oscillator IC, investigating....
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Check for a 180-degree rotation of the part ... darned rotationally symmetric parts ... :)
Cheers,
Dave