I seem to have a communications problem describing my problem.
I think the home position is the left rear corner aka Y max and X
min. My controller is a SmoothieBoard with a reprap discount LCD panel.
The home XYZ command from the panel results in a move to the home position 0, 195. (and z 0 which is full up).
I described movements toward the front of the printer, to lower Y positions, as a movement in the negative direction. Movement to increasing y positions, to the rear of the printer, is a move in a positive direction.
Movement in x is positive moving to the right.
When my printer is powered on, the position shows as 0,0.
On my printer after homing all axis (moving to the left rear corner ) the panel shows the position as 0,195.
Since I can reproduce the problem from the panel without executing any G-code I don't think it could be my start G-code.
Before using the panel "Home All Axis" command: If the printer is powered on with the extruder in the middle of the print bed Y Jog commands move on the diagonal. Negative Y jog commands move toward the front right corner. X Jog commands work correctly.
After using the panel "Home all axis" command: using the panel to jog the Y axis results in a move in the x axis only with the direction inverted. Negative Y movement moves the extruder to the right. X Jog commands work correctly.
I have not added any custom start code to slic3r. I used the slic3r default without thinking about it:
G28 ; home all axes
G1 Z5 F5000 ; lift nozzle
Could you post a g-code file for a simple test object? This would be useful for early testing and differentiate between a slicer program configuration problem and a firmware/hardware problem.