I started making a protoboard prototype of a device that uses arduino mega. Then I integrated what I had in the protoboard, with the available schematic of the arduino mega in a KiCad board design, and had it manufactured.
I couldn't board the boot-loader albeit the other components in the board worked well (i.e. addressable led's). While troubleshooting, I measured the clock pins. In a healthy arduino uno, I saw that there was a 1volt oscillation starting at 0v. Then, I measured my custom board, and the oscillation is the same, only that it starts at 1v. No wonder why I couldn't burn bootloader. I was powering the bricked arduino with a healthy arduino uno, pin to pin.
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I discovered in many other points of the board, ground is 1V despite it is connected pin-by pin to an arduino uno whose voltage levels are ok. They are hooked up via the 6-pin ISCP (MOSI, MISO, 6V, SCL, GND, SS)
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I am tying to figure out what was my mistake, perhaps with some jumper wires I could correct it.
I attached the crystal section of my schematic, and photos of the oscilloscopes. I know little what could be the cause, so I don't know what else to attach.
my crystal datasheet: https://statics3.seeedstudio.com/images/opl/datasheet/306010014.pdf
C8 and C9 datasheets: https://statics3.seeedstudio.com/images/opl/datasheet/302010018.pdf
thanks for checking this!