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As I cannot dissociate VCCIO and VCC on the PCBs, I made some trials on a fresh board powered by a single 1.2V supply and there is no more short-circuit. My USB blaster isn't compatible with 1.2V I/O levels so I need to add a level shifter circuit prior to test if JTAG is properly operating.
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I think you are still in trouble if you can't split VCCA from the other supplies. 1.2V is OK as VccIO, but VccA is still required at 2.5V.
I've long been irritated by the need to provide the 2.5V nominally for the PLLs even if I'm not using the PLL; I haven't tried it on MAX10, but certainly on older Altera families (Cyclone 2/3) it won't boot without the 2.5V being at the right voltage, even if you don't use the PLL after boot. Possibly the 2.5V also runs the internal oscillator that clocks the boot process.
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