Firmware. It's probably thinking it's hit a software endstop.
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www.instructables.com]
Try here, start from the beginning but page 3 sounds like it's where you're running into an issue.
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Configuring Marlin firmware in Arduino IDE
Open the Configuration.h file/sketch/tab and scroll Down to the @section homing - around line 330 or so.
Make sure you do not have 2 // in front of #define ENDSTOPPULLUPS. If you have, then remove them, upload the firmware to your printer and redo the tests we just did in Pronterface.
Note: remmeber you have to discconnect in Pronterface before uploading firmware or you will get an error in Arduino IDE