Here is your problem, the position block is at 5 pixels not 5 blocks.
However, I don’t really like this system, it means you have to manually set respawn for each other the checkpoints. If you want it to just save automaticly, then use this code:
{"data":{"behavior":{"v":"2","nodes":[{"inputCount":0,"outputCount":0,"name":"Checkpoint","behaviorType":"logic.NodeGroup","x":-720,"y":-136,"group":"","id":"2a5cf6132497ba49","isMenuItem":false},{"inputCount":0,"outputCount":1,"name":"Once","behaviorType":"logic.triggers.Once","x":-540,"y":0,"group":"2a5cf6132497ba49","id":"255c6d4c29d47e4e","resetOnLevelStart":false},{"inputCount":2,"outputCount":1,"name":"Save Number","behaviorType":"logic.logic.Storage","x":-360,"y":-72,"group":"2a5cf6132497ba49","id":"255cc123d225c441","storageKey":"Checkpoint X","dataType":2},{"inputCount":2,"outputCount":1,"name":"Save Number","behaviorType":"logic.logic.Storage","x":-360,"y":24,"group":"2a5cf6132497ba49","id":"2a5a137aefcfd24d","storageKey":"Checkpoint Y","dataType":2},{"inputCount":4,"outputCount":2,"name":"Position","behaviorType":"logic.properties.Position","x":-180,"y":0,"group":"2a5cf6132497ba49","id":"2a5a72f04573f143","pixelUnits":true,"resetVelocity":false},{"inputCount":1,"outputCount":1,"name":"Extractor","behaviorType":"logic.properties.Extractor","x":-360,"y":200,"group":"2a5cf6132497ba49","id":"2a5adf822c67a644","targetId":0,"prop":"x","version":2},{"inputCount":1,"outputCount":1,"name":"Extractor","behaviorType":"logic.properties.Extractor","x":-360,"y":304,"group":"2a5cf6132497ba49","id":"2a5ae54edd794f48","targetId":0,"prop":"y","version":2},{"inputCount":2,"outputCount":1,"name":"Save Number","behaviorType":"logic.logic.Storage","x":-180,"y":176,"group":"2a5cf6132497ba49","id":"2a5b35db22f6fe47","storageKey":"Checkpoint X","dataType":2},{"inputCount":2,"outputCount":1,"name":"Save Number","behaviorType":"logic.logic.Storage","x":-180,"y":312,"group":"2a5cf6132497ba49","id":"2a5b3680a2d8974b","storageKey":"Checkpoint Y","dataType":2},{"inputCount":0,"outputCount":1,"name":"Always","behaviorType":"logic.triggers.Always","x":-900,"y":256,"group":"2a5cf6132497ba49","id":"2a5c3520e8b56547"},{"inputCount":2,"outputCount":3,"name":"Proximity","behaviorType":"logic.components.Prox2","x":-720,"y":240,"group":"2a5cf6132497ba49","id":"2a5c44acd8626d42","targetEntityId":0,"threshold":10,"targetClassId":17582767,"nearestOnly":false,"firstObject":true,"allObjects":false,"contains":false,"shape":0,"oX":0,"oY":0,"pin":false},{"inputCount":3,"outputCount":1,"name":"Switch","behaviorType":"logic.logic.Switch","x":-540,"y":240,"group":"2a5cf6132497ba49","id":"2a5c84e3c6b61645","_startVal":0,"dataType":2}],"links":[{"input_id":"255cc123d225c441i1","output_id":"255c6d4c29d47e4eo0"},{"input_id":"2a5a137aefcfd24di1","output_id":"255c6d4c29d47e4eo0"},{"input_id":"2a5a72f04573f143i0","output_id":"255cc123d225c441o0"},{"input_id":"2a5a72f04573f143i1","output_id":"2a5a137aefcfd24do0"},{"input_id":"2a5b35db22f6fe47i0","output_id":"2a5adf822c67a644o0"},{"input_id":"2a5b3680a2d8974bi0","output_id":"2a5ae54edd794f48o0"},{"input_id":"2a5c44acd8626d42i1","output_id":"2a5c3520e8b56547o0"},{"input_id":"2a5c84e3c6b61645i2","output_id":"2a5c44acd8626d42o0"},{"input_id":"2a5c84e3c6b61645i1","output_id":"2a5c44acd8626d42o2"},{"input_id":"2a5adf822c67a644i0","output_id":"2a5c84e3c6b61645o0"},{"input_id":"2a5c84e3c6b61645i0","output_id":"2a5c84e3c6b61645o0"},{"input_id":"2a5ae54edd794f48i0","output_id":"2a5c84e3c6b61645o0"}]}}}
Delete the code you had for checkpoint in the player object and replace it with the code above. Now you can have multiple checkpoints without presetting the respawn point for each one.