<font face="Arial, Verdana" size="2">It </font>Slic3r also supports more than 4 extruder, if you use all 4 are then used in the right order, but if you use 1 or 2 or 3 repetier always uses from 0 onwards.
<font face="Arial, Verdana" size="2">If I do it directly from SLic3r and then import the gcode used in repetier see the right extruder. I think it's a problem of commands that are sent to slic3r. </font>
<font face="Arial, Verdana" size="2">I did a test with CURE (used Extruder 2 and 4), in the gcode I have the settings of the temperature of the extruder right, but then they are always used T0 and T1 ...</font>