G21
G90
G00 Z30.0000 
M03
G04 P2.000000
G00 X-30.5590 Y31.9900 // First move XY directly to the first position of the job, not to X0, Y0
G00 Z2.0000  // And after the XY-Move it comes the Z-Move to Z-Up
G01 Z-0.1000 F254   
G01 X-30.5972 Y31.8978 F508   
G01 X-30.6678 Y31.8272

void begin_gcode(void)
{
	out(get_mode());

	cur_x = -999.999; // I think you forgot it?!...
	cur_y = -999.999; // ...Its important that the cur_positions are "cleared"... 
	cur_z = -999.999; // ...before starting a new file.

	out(ABSOLUTE_MODE);
	rz(DEFAULT_Z_HIGH); // Here the Move of Z first!
	//rxy(X_HOME, Y_HOME); // This is not needed, i think...
	out(fr(SPINDLE_ON, SPINDLE_ON_TIME));
}

if (DO_TOOL_CHANGE_WITH_ZERO_STEP == YES) {
		rxy(TOOL_CHANGE_POS_X, TOOL_CHANGE_POS_Y); // This I added
		output_tool_zero_begin();
		fzr(0.000, FEED_RATE_Z);
		out(fir(TOOL_CHANGE, m_current_tool, drill_size));
		output_tool_zero_end();
		rz(DEFAULT_Z_UP); // This I added
	}

	rxy(drill_x, drill_y); // This I added -> First move to the XY position, after that it comes the Z-Move
	out(fr(SPINDLE_ON, SPINDLE_ON_TIME)); // This i moved from two lines below to here
	rz(DEFAULT_Z_UP);
	//out(fr(SPINDLE_ON, SPINDLE_ON_TIME)); // see two lines before...
	output_tool_change_end();

case ST_START_LINE:
			user_track_begin(rx1, ry1, rx2, ry2);

			m_lines += coords(rx1, ry1, rx2, ry2);

			if (cur_z != DEFAULT_Z_DOWN) // This i added
				rxy(rx1, ry1); // This i added (Move XY before Move Z)
			rz(DEFAULT_Z_UP);
			rxy(rx1, ry1);
			fzr(z_down, FEED_RATE_Z);
			fxyr(rx2, ry2, FEED_RATE);
			pair_count = 0;
			break;

	case ST_ARC_END:
			user_arc_end(rx1, ry1, rx2, ry2);
			real cx = rx2;
			real cy = ry2;
			real end_x = rx1;
			real end_y = ry1;
		
			if (1 /* USE_IJ_RELATIVE */) {
				cx = rx2 - rx1;
				cy = ry2 - ry1;
			}

			if (cur_z != DEFAULT_Z_DOWN) // Here the same...
				rxy(rx1, ry1); // ...as above

			rz(DEFAULT_Z_UP);
			rxy(end_x, end_y);
			fzr(z_down, FEED_RATE_Z);
			if (g_side == TOP || MIRROR_BOTTOM == YES) {
				out(frrrr(CIRCLE_TOP, m_arc_begin_x, m_arc_begin_y, cx, cy));
			}
			else {
				out(frrrr(CIRCLE_BOTTOM, m_arc_begin_x, m_arc_begin_y, cx, cy));
			}
			break;

dlgGroup("Tool Change") {
				dlgGridLayout {
					dlgCell(1, 0) dlgLabel("Position X ");
					dlgCell(1, 1) { dlgRealEdit(TOOL_CHANGE_POS_X); 
						dlgLabel(m_uom_suffix, YES); 
					}
					dlgCell(2, 0) dlgLabel("Position Y ");
					dlgCell(2, 1) { dlgRealEdit(TOOL_CHANGE_POS_Y); 
						dlgLabel(m_uom_suffix, YES); 
					}
					dlgCell(3, 0) dlgLabel("Position Z ");
					dlgCell(3, 1) { dlgRealEdit(TOOL_CHANGE_POS_Z); 
						dlgLabel(m_uom_suffix, YES); 
					}
					dlgCell(4, 0) { dlgCheckBox("Use Machine Coordinates  ", USE_MACHINE_COORDINATES_FOR_TOOL_CHANGE); //Here is the new Checkbox
					}
					
				}
			}

if (drill_size == last_size) {
					output_drill_hole(drill_x, drill_y, DRILL_DEPTH);
				}
				else {
					m_current_tool++;
					output_tool_change_begin();
					out(SPINDLE_OFF);
					if (USE_MACHINE_COORDINATES_FOR_TOOL_CHANGE == YES) { // This I added
						rz_mc(TOOL_CHANGE_POS_Z);	// This I added
						rxy_mc(TOOL_CHANGE_POS_X, TOOL_CHANGE_POS_Y); // This I added
					} // This I added
					else { // This I added 
						rz(TOOL_CHANGE_POS_Z); 
						rxy(TOOL_CHANGE_POS_X, TOOL_CHANGE_POS_Y);
					} // This I added
					out(fir(TOOL_CHANGE, get_tool_num_for(my_strtol(drill_args[DRILL_SIZE]), m_current_tool), drill_size));
					output_tool_changed();

// Move Z in machine coordinates
void rz_mc(real z)
{
	
	out(MACHINE_COORDINATES + fr(RAPID_MOVE_Z, z) + EOL);
	cur_z = 999.99; // Very important, because the "real"-Position (Not-Machine-Position) is not well-known!!

}

// Move XY in machine coordinates
void rxy_mc(real x, real y)
{
	out(MACHINE_COORDINATES +  frr(RAPID_MOVE_XY, x, y)               + EOL);
	cur_x = 999.99;
	cur_y = 999.99;
}