It does sound strange, the fact the even with the circuits disconnected and limits enabled would suggest to me that it may well be a setup issue, double check(am sure you have but lets humour me) the pin and port number you have set for all your limit input and motor signals to make sure you haven't used the same pin number twice.
Am not expert so outside of that I have no other advice.
Maybe post a quick sketch of how you wired it all up incase there is something wrong and you are pulling the port down, although this is unlikely.
Rob
edit: reread your post and you say it doesnt happen when jogging, mmm maybe post a screen shots of your config screens and someone might be able to spot something.


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