I just finished wiring my LR3 and am seeing the similar weirdness that the OP (@chrywo ) is seeing. I am 100% confident in my soldering and wiring. I, too, see the appropriate board SMT LEDs turn on/off when I manually trigger individual switches. I am testing via the TFT touchscreen terminal on the SKR Pro with 2209s.
I’ve done the same debugging steps of removing all of the endstop connectors on the board and then reconnecting them. Once I’m confident in the connections I hot-glued them in position. The board is mounted in the case.
My X endpoint appeared to be working via the M119 command. I homed it a couple of times with success and then it failed and started grinding into the sideplate.
Another oddity, Y2min. If I close the non-rail Y2min endpoint switch, push the reset button and reboot, and execute M119, Y2min registers as TRIGGERED. I release the switch and retest M119, it register open. If I close the Y2min switch again and retest M119, it shows open!? This behavior is repeatable. Booting with the switch closed shows TRIGGERED, but will never show TRIGGERED again.
I am using FW version 513DL from the V1Engineering release on github.
Not sure where to go next. I realize I can use the machine without endstops but this problem is troubling. I’ve spent my career designing/building/testing/producing scientific instrumentation. This build is definitely in my wheelhouse. Something seems very inconsistent in the behavior.