I'm no expert but if you want a quick answer, it appears that there are two setups for the limits. Normally open and normally closed. It's something in the SB software you can change to make it match your machine. Typically, (this is from memory, not knowledge) you can make a choice when you install the SB software that will select the right base settings. You probably took the wrong option.
If you have the time, just search through the SB software settings, find where the limit switches are setup and switch from whatever it is now to the "other" setting. Should take care of it.
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