I’ve seen three topics on this forum where endstops on the SKR Pro board are failing to trigger inside Marlin. I’m not sure we ever got to the root of the problem with these other topics, but the best guess was a manufacturing problem with the board that results in pins not reading high when they should. One person fixed the issue by adding 1.5K pullup resistors between the signal pin and 5V pin of each endstop plug. It is too early in the trouble shooting process to say this is what is going on with your board, but I wanted to make you aware of the potential issue.
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