Reverse Engineer a System

I have a pallet pool system but don't have the PLC program. I'm trying to work out the Y axis logic by its behavior. The mechanics consist of just two limit switches. These seem to control not only the end of travel but also the direction for travel. If the switch (-) minus is made it moves (+) plus and the opposite is true when the (+) switch is made under automatic control only. At some point in the operation it gets confused and won't move under automatic control. The LEDs on the PLC that indicates the status are both out even though Y (-) switch is made. The manual jog box won't operate unless the Y (-) minus switch manually opened. Here's where it gets weird. While jogging the axis manually in the (+) plus direction (using the + button) at some point in the travel the motion reverses direction and you must use the (-) minus button the move (+) plus until the (+) plus switch is made. Then the the buttons on the jog box and the direction of travel match. After this manual operation the will work under automatic control. The switches are good but replaced them only to find the old switches test fine on the bench. There seems to be something in the PLC logic that governs this behavior. Any idea of what the underlying logic is here?