Biglia Eurotech 436 Y2 lathe B-axis homing issue

Hello, I have a strange issue that occurs randomly maybe once every other week on our Eurotech CNC lathe. The machine has a B-axis which is controlled by head 1 ( is essentially a z-axis for the sub spindle). In the program we call up a G28 to home all the axis' before calling up the pickoff arm to avoid collisions. What happens is the B-axis will start going home then stop 3.00" before the home position. It shows it's 0.00 on both the relative and absolute position coordinates, but not the machine coordinate. The machine coordinate will show 3.00". The pickoff arm will come out to grab the part, then it will collide with the B-axis because it's not back at its home position. Usually you can't move the pick off arm unless the axis' are in their home positions. It does this very sporadically. Anyone have any ideas on what could possibly be causing this problem?