So last night, I stripped down the gcode file I was trying to print to just one layer and removed all the extrudes, just to see what would happen with and without the BOM (just to rule that out). I got the same behavior. I'll post some of the beginning of that log file below.
I then started a print from the SD card via a script which allows me to capture the output from the printer. I'll put the beginning of the gcode file from the SD card and the messages that were being received from the printer.
I'll try the two commands you posted above to see what happens. BTW, my communication timeout in the RS UI shows 3 seconds. I'm not sure if that's the default or if I ever modified that value or not.
Beginning of logfile from a no BOM version of the gcode
< 2:40:22.631: N18 M532 X0.0000 L0
< 2:40:22.639: N19 M532 X0 L0
> 2:40:22.640: ok
< 2:40:22.641: N20 M531 bom-test-3
< 2:40:22.641: N21 M530 S1 L0
> 2:40:22.651: ok
> 2:40:22.651: ok
> 2:40:22.652: ok
< 2:40:22.726: N22 M107
< 2:40:22.727: N23 M532 X0.4424 L0
< 2:40:22.727: N24 M190 S80 ; set bed temperature
< 2:40:22.728: N25 M532 X0.8849 L0
< 2:40:22.729: N26 M104 S200 ; set temperature
> 2:40:22.731: T:26.94 /0.00 B:29.51 /0.00 @:0 B@:0
> 2:40:22.735: ok
> 2:40:22.736: ok
< 2:40:22.737: N27 M532 X1.3274 L0
> 2:40:22.740: T:26.94 /0.00 B:29.51 /80.00 @:0 B@:0 W:?
> 2:40:23.723: T:27.00 /0.00 B:29.49 /80.00 @:0 B@:127
> 2:40:23.743: T:27.00 /0.00 B:29.49 /80.00 @:0 B@:127 W:?
> 2:40:24.722: T:26.97 /0.00 B:29.74 /80.00 @:0 B@:127
> 2:40:24.743: T:26.97 /0.00 B:29.74 /80.00 @:0 B@:127 W:?
> 2:40:25.722: T:27.00 /0.00 B:29.97 /80.00 @:0 B@:127
> 2:40:25.742: T:27.00 /0.00 B:29.97 /80.00 @:0 B@:127 W:?
> 2:40:26.722: T:27.00 /0.00 B:30.34 /80.00 @:0 B@:127
> 2:40:26.741: Warning: Communication timeout - resetting communication buffer.
> 2:40:26.742: Connection status: Buffered:80, Manual Commands: 1, Job Commands: 214
> 2:40:26.742: Buffer used:80 Enforced free byte:17 lines stored:4
< 2:40:26.742: M117 ETA 02:36:47 day 22
> 2:40:26.743: T:27.00 /0.00 B:30.34 /80.00 @:0 B@:127 W:?
< 2:40:26.743: N28 M109 S200 ; wait for temperature to be reached
< 2:40:26.743: N29 M532 X1.7699 L0
< 2:40:26.744: N30 G21 ; set units to millimeters
> 2:40:27.721: T:26.97 /0.00 B:30.70 /80.00 @:0 B@:127
> 2:40:27.741: T:26.97 /0.00 B:30.70 /80.00 @:0 B@:127 W:?
> 2:40:28.721: T:27.03 /0.00 B:31.12 /80.00 @:0 B@:127
> 2:40:28.741: T:26.97 /0.00 B:31.21 /80.00 @:0 B@:127 W:?
> 2:40:29.737: T:26.91 /0.00 B:31.60 /80.00 @:0 B@:127
Beginning gcode from SD card
M107
M190 S125
M104 S255
M109 S255
G21
G90
M82
G92 E0
G10
G92 E0
G1 Z0.32 F7800
G1 X83.943 Y80.601 F7800
G11
G92 E0
G1 X85.59 Y79.651 E0.14623 F1200
G1 X87 Y79.429 E0.25596
G1 X107 Y79.429 E1.79368
G1 X108.86 Y79.824 E1.9399
Captured printer output when printing above SD card file
echo:Now fresh file: RIPTEST.GCD
File opened: RIPTEST.GCD Size: 429683
File selected
ok
ok
T:30.34 /0.00 B:120.05 /125.00 @:0 B@:64 W:?
T:30.34 /0.00 B:120.00 /125.00 @:0 B@:127 W:?
T:30.34 /0.00 B:120.15 /125.00 @:0 B@:127 W:?
T:30.39 /0.00 B:120.30 /125.00 @:0 B@:127 W:?
...
T:30.69 /0.00 B:125.00 /125.00 @:0 B@:84 W:2
T:30.69 /0.00 B:125.00 /125.00 @:0 B@:89 W:1
T:30.69 /0.00 B:125.00 /125.00 @:0 B@:92 W:0
T:30.69 /255.00 B:125.00 /125.00 @:0 B@:94 W:?
T:30.69 /255.00 B:125.00 /125.00 @:127 B@:96 W:?
T:30.97 /255.00 B:125.00 /125.00 @:127 B@:97 W:?
T:31.72 /255.00 B:125.00 /125.00 @:127 B@:98 W:?
T:33.02 /255.00 B:125.17 /125.00 @:127 B@:65 W:?
T:35.13 /255.00 B:125.17 /125.00 @:127 B@:64 W:?
T:37.93 /255.00 B:125.17 /125.00 @:127 B@:61 W:?
...
T:256.67 /255.00 B:125.00 /125.00 @:17 B@:75 W:2
T:255.00 /255.00 B:125.00 /125.00 @:49 B@:75 W:1
T:255.00 /255.00 B:125.00 /125.00 @:47 B@:75 W:0
X:189.00 Y:184.00 Z:10.00 E:0.00 Count X:30240 Y:29440 Z:80000
X:189.00 Y:184.00 Z:10.00 E:0.00 Count X:30240 Y:29440 Z:80000
X:83.94 Y:80.60 Z:0.32 E:0.00 Count X:30240 Y:29440 Z:78200
echo:busy: processing
echo:busy: processing
X:83.91 Y:80.65 Z:0.32 E:0.00 Count X:17818 Y:13230 Z:2132
X:103.89 Y:100.89 Z:0.32 E:0.00 Count X:17847 Y:16659 Z:2070
echo:busy: processing
echo:busy: processing
echo:busy: processing
echo:busy: processing
X:105.76 Y:85.52 Z:0.32 E:0.00 Count X:16344 Y:13882 Z:2142