Replicator 2X Cura definition - slightly tweaked for my printer, which is running Sailfish

makerbot_rep2x_1st.def.json

{
    "id": "makerbot_rep2x_1st",
    "version": 2,
    "name": "Rep2X Right Extruder",
    "inherits": "fdmextruder",
    "metadata": {
        "machine": "makerbot_replicator_2x",
        "position": "0"
    },

    "overrides": {
        "extruder_nr": {
            "default_value": 0,
            "maximum_value": "1"
        },
        "machine_nozzle_offset_x": { "default_value": 0.0 },
        "machine_nozzle_offset_y": { "default_value": 0.0 },

        "machine_extruder_start_pos_abs": { "default_value": true },
        "machine_extruder_start_pos_x": { "value": "prime_tower_position_x" },
        "machine_extruder_start_pos_y": { "value": "prime_tower_position_y" },
        "machine_extruder_end_pos_abs": { "default_value": true },
        "machine_extruder_end_pos_x": { "value": "prime_tower_position_x" },
        "machine_extruder_end_pos_y": { "value": "prime_tower_position_y" }
    }
}

makerbot_rep2x_2nd.def.json

{
    "id": "makerbot_rep2x_2nd",
    "version": 2,
    "name": "Rep2X Left Extruder",
    "inherits": "fdmextruder",
    "metadata": {
        "machine": "makerbot_replicator_2x",
        "position": "1"
    },

    "overrides": {
        "extruder_nr": {
            "default_value": 1,
            "maximum_value": "1"
        },
        "machine_nozzle_offset_x": { "default_value": 0.0 },
        "machine_nozzle_offset_y": { "default_value": 0.0 },

        "machine_extruder_start_pos_abs": { "default_value": true },
        "machine_extruder_start_pos_x": { "value": "prime_tower_position_x" },
        "machine_extruder_start_pos_y": { "value": "prime_tower_position_y" },
        "machine_extruder_end_pos_abs": { "default_value": true },
        "machine_extruder_end_pos_x": { "value": "prime_tower_position_x" },
        "machine_extruder_end_pos_y": { "value": "prime_tower_position_y" }
    }
}

makerbot_replicator_2x.def.json

{
    "id": "makerbot_replicator_2x",
    "version": 2,
    "name": "MakerBot Replicator 2X",
    "inherits": "fdmprinter",
    "metadata": {
        "visible": true,
        "author": "TheUltimakerCommunity",
        "manufacturer": "MakerBot",
        "category": "Other",
        "file_formats": "application/x3g",
        "platform_offset": [ 0, 0, 0 ],
        "has_materials": true,
        "preferred_material": "*generic_abs_175*",
        "machine_extruder_trains": {
            "0": "makerbot_rep2x_1st",
            "1": "makerbot_rep2x_2nd"
        },
        "supported_actions": [ "MachineSettingsAction" ],
        "supports_usb_connection": true,
        "machine_x3g_variant": "r2x"
    },
    "overrides": {
        "machine_name": { "default_value": "MakerBot Replicator 2X" },
        "machine_gcode_flavor": {
            "default_value": "Makerbot"
        },
        "machine_acceleration": {
            "default_value": 3000
        },
        "machine_width": {
            "default_value": 246
        },
        "machine_depth": {
            "default_value": 152
        },
        "machine_height": {
            "default_value": 155
        },
        "gantry_height": {
            "default_value": 60,
            "comment": "This needs to be filled in"
        },
        "machine_nozzle_head_distance": {
            "default_value": 3,
            "comment": "This needs to be filled in"
        },
        "machine_heat_zone_length": {
            "default_value": 16,
            "comment": "This needs to be filled in"
        },
        "machine_heated_bed": {
            "default_value": true
        },
        "machine_max_feedrate_x": {
            "default_value": 300
        },
        "machine_max_feedrate_y": {
            "default_value": 300
        },
        "machine_max_feedrate_z": {
            "default_value": 19.5
        },
        "machine_max_feedrate_e": {
            "default_value": 26
        },
        "machine_center_is_zero": { "default_value": true },
        "machine_extruder_count": {
            "default_value": 2
        },
        "machine_start_gcode": {
            "default_value": "; -- START GCODE Rep2x -- \n; begin print\nM136 ;(enable build)\nM73 P0 ;(set build percentage to zero)\n; homing\nG162 X Y F2000 ;(home XY axes maximum, standard feedrate 2000 mm/min)\nG161 Z F900 ;(home Z axis minimum, standard feedrate 900 mm/min)\nG92 X0 Y0 Z-5 A0 B0 ;(set Z to -5)\nG1 Z0.0 F900 ;(move Z to '0', standard feedrate 900 mm/min)\nG161 Z F100 ;(home Z axis minimum, standard feedrate 100 mm/min)\nM132 X Y Z A B ;(Recall stored home offsets for XYZAB axis)\n; set start position\nG92 X152 Y72 Z0 A0 B0 ;(set zero for X and Y)\nG1 X-112 Y-73 Z150 F3300.0 ;(move to waiting position, standard feedrate 3300 mm/min)\nG130 X20 Y20 A20 B20 ;(Lower stepper Vrefs while heating)\n; heat platform\nM109 S{material_bed_temperature} T0 ;(Set build platform temperature in degrees Celsuis)\nM134 T0 ;(Wait for platform to heat up)\n; EXTRUDER HEAT BEGIN\nM135 T0 ;(Set the extruder as the current Extruder)\nM104 S{material_print_temperature} T0 ;(Set extruder temperature in degrees Celsius)\nM133 T0 ;(Wait for extruder to heat up)\n; end start sequence\nG130 X127 Y127 A127 B127 ;(Set Stepper motor Vref to defaults)\n; initial purge\nG92 A0 ;zero the extruded length\n; -- END OF START GCODE --"
        },

        "machine_end_gcode": {
            "default_value": "; -- END GCODE -- \n; end position\nM18 A B ;(Turn off A and B Steppers)\nG1 Z{machine_height} F900 ;(Move Z to machine_height, feedrate 900 mm/min)\nG162 X Y F2000 ; (Home Z Axis Maximum, feedrate 2000 mm/min)\nM18 X Y Z ;(Turn off steppers after a build)\n; cool bed\nM140 S0 T0 ;(Cool Bed)\n; cool extruders\nM104 S0 T0 ;(Cool Right extruder)\n; end print\nM73 P100 ;(end  build progress)\nM70 P5 ;(We <3 Making Things!)\nM72 P1 ;( Play Ta-Da song )\nM137 ;(build end notification)"
        },
        "retraction_amount": {
            "default_value": 2
        },
        "retraction_speed": {
            "default_value": 25
        },
        "material_diameter": { "default_value": 1.75 },
        "default_material_print_temperature": { "default_value": 230 },
        "material_print_temperature_layer_0": { "default_value": 0 },
        "material_initial_print_temperature": {
            "enabled": false,
            "value": "max(-273.15, material_print_temperature)",
            "default_value": "max(-273.15, material_print_temperature)"
        },
        "material_final_print_temperature": {
            "enabled": false,
            "value": "max(-273.15, material_print_temperature)",
            "default_value": "max(-273.15, material_print_temperature)"
        },
        "material_bed_temperature": {
            "default_value": 120,
            "maximum_value_warning": "150"
        },
        "material_bed_temperature_layer_0": {
            "default_value": "material_bed_temperature",
            "maximum_value_warning": "150",
            "enabled": false
        },
        "speed_print": { "default_value": 100 },
        "speed_travel": {
            "default_value": 175
        },
        "speed_layer_0": {
            "value": "speed_print * 30 / 90"
        },
        "acceleration_enabled": { "enabled": false },
        "jerk_enabled": { "enabled": false },
        "adhesion_type": { "default_value": "raft" },
        "raft_margin": { "default_value": 3 }
    }
}

it may also be a firmware difference - whether you're using a newer sailfish or not. At least in newer sailfish, the eeprom value meaning changes. Both my extruder offsets are approximately 0. I upgraded to a newer sailfish very shortly after getting my machine, so I've never really tested any of these configs on their old outdated firmware.