$ s3g-decompiler.py forum.x3g
Command count: (Command ID) Command description
1: (153) Start build notification, steps 0, name "forum"
2: (150) Set build percentage 0%, reserved 0
3: (134) Switch to Tool 0
4: (132) Home maximum on X, Y, feedrate 361 us/step, timeout 20 s
5: (131) Home minimum on Z, feedrate 136 us/step, timeout 20 s
6: (140) Define position as (0, 0, -2000, 0, 0)
7: (155) Move to (0, 0, 0, 0, 0), DDA rate 7799, X, Y, A, B relative, distance 5.000000 mm, feedrate*64 1248 steps/s
8: (131) Home minimum on Z, feedrate 1500 us/step, timeout 20 s
9: (144) Recall home position for X, Y, Z, A, B
10: (139) Absolute move to (-12235, -7059, 12000, 0, 0) with DDA 70
11: (145) Set X axis digipot to 20
12: (145) Set Y axis digipot to 20
13: (145) Set Z axis digipot to 20
14: (145) Set A axis digipot to 20
15: (145) Set B axis digipot to 20
16: (136) Tool 0: (13) Toggle blower fan 0
17: (136) Tool 0: (31) Set build platform temperature to 110 C
18: (141) Wait until platform 0 is ready, 100 ms between polls, 65535 s timeout
19: (136) Tool 1: (3) Set target temperature to 230 C
20: (135) Wait until Tool 1 is ready, 100 ms between polls, 65535 s timeout
21: (145) Set X axis digipot to 127
22: (145) Set Y axis digipot to 127
23: (145) Set Z axis digipot to 40
24: (145) Set A axis digipot to 127
25: (145) Set B axis digipot to 127
26: (140) Define position as (-12235, -7059, 12000, 0, 0)
27: (134) Switch to Tool 1
28: (139) Absolute move to (-12235, -7059, 12000, 0, 0) with DDA 70
29: (155) Move to (-9412, -6118, 12000, 0, 0), DDA rate 13395, A, B relative, distance 31.622776 mm, feedrate*64 9600 steps/s
30: (155) Move to (-9412, -6118, 120, 0, 0), DDA rate 7800, A, B relative, distance 29.700001 mm, feedrate*64 1248 steps/s
31: (155) Move to (8471, -6118, 120, 0, -2311), DDA rate 3137, A, B relative, distance 190.000000 mm, feedrate*64 2133 steps/s
32: (155) Move to (9412, -6118, 120, 0, 0), DDA rate 282, A, B relative, distance 10.000000 mm, feedrate*64 192 steps/s
33: (155) Move to (10353, -6118, 120, 0, 0), DDA rate 7841, A, B relative, distance 10.000000 mm, feedrate*64 5333 steps/s
34: (155) Move to (10353, -6118, 400, 0, 0), DDA rate 666, A, B relative, distance 0.700000 mm, feedrate*64 106 steps/s
35: (140) Define position as (10353, -6118, 400, 0, 0)
36: (158) Pause @ Z position 2.000000
37: (150) Set build percentage 1%, reserved 0
38: (155) Move to (10353, -6118, 400, 0, 97), DDA rate 1920, A, B relative, distance 1.000000 mm, feedrate*64 1280 steps/s
39: (150) Set build percentage 100%, reserved 0
40: (154) End build notification, options 0x00
EOF
It looks like the Pause is emitted where you'd expect. It also gets emitted with gpx1.3 which I think is close to the one that s3d is using. Do you have an x3g that S3D outputs using this gcode? I could run the decompiler on it and see if it shows up.
Are you printing from the SD card using the LCD panel or are you driving the print over USB with S3D?