<font face="Arial, Verdana">S1000 gets ignored. Just run a test </font>
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S1000
M117 Hi
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<font face="Arial, Verdana">on Repetier-Host with this result:</font>
<font face="Arial, Verdana">10:11:02.865 : N41 M45122</font>
<font face="Arial, Verdana">10:11:02.865 : N42 S1000*26</font>
<font face="Arial, Verdana">10:11:02.865 : Printjob finished at 19.05.2016 10:11</font>
<font face="Arial, Verdana">10:11:02.865 : Printing Time: 0s</font>
<font face="Arial, Verdana">10:11:02.865 : Lines Send: 5</font>
<font face="Arial, Verdana">10:11:02.890 : N43 M117 Hi18</font>
<font face="Arial, Verdana">10:11:02.893 : N44 M104 T0 S0*17</font>
<font face="Arial, Verdana">10:11:02.893 : N45 M104 T1 S017</font>
<font face="Arial, Verdana">10:11:02.893 : N46 M84*45</font>
<font face="Arial, Verdana">10:11:02.975 : Disabled volumetric extrusion for extruder 0</font>
<font face="Arial, Verdana">10:11:02.975 : Disabled volumetric extrusion for extruder 1</font>
<font face="Arial, Verdana">10:11:02.976 : PrinterMode:FFF</font>
<font face="Arial, Verdana">10:11:02.981 : Unknown command:N42 S1000</font>
<font face="Arial, Verdana">10:11:03.158 : Successfully send push message.</font>
As you see firmware detected it as unknown command and next line was send.
What did you use for sending it? Maybe the host/firmware combination makes a difference.
There is no branch to handle S only commands. We only support G/M/T as command identifier. Everything else gets ignored.