Sounds like the Z axis end stop maybe unplugged. Check the wire leading from the end stop that is attached to the side of the platform.
If everything is connected use the code M119 in the g-code entry of the manual control tab to see the current status.
SD3 w/ mods:
Glass bed with QU-BD heat pad upgrade, threadless ballscrew w/ 8mm smooth rod, spectra line belt replacement, lawsy MK5 extruder, Lawsy replacement carriage, E3D hotend, Ramps 1.4 w/ reprap discount controller, DRV8825 drivers, 12v 30A PS, Acrylic case, Overkill Y-idlers, Filament alarm, Extruder fan + more.