I was having a similar issue with an avoton super micro motherboard (A1SRM- 2758) and then I realised the pinout shown for power and LEDs is inverted to the picture shown on the motherboard so I had the power and LEDs connected wrongly ... Doh! Just in case you did what I did which is easy with the manual provided, the dark pin on JF1 is pin 1 but with the closeup view on my manual they had pin 1 bottom right when should be top left if that makes sense.
So now I don't have to turn on by IPMI but it was really cool to get to use IPMI which I might have not before .
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