The following issues tend to arise on Thing-o-Matic and Cupcake printers.
This is normal — just set the extruder count to the correct count of either 1 or 2 via ReplicatorG’s “Onboard Preferences” item found under the “Machine” menu. You will first need to connect your printer to ReplicatorG over USB.
This typically results from running the Z axis too fast resulting in lost steps. As a result, the printer thinks the extruder is very close to the build platform when in reality it is very far away.
There are two typical causes for this. On Thing-o-Matics, it is often that the Z-axis is binding. Clean the Z rods, lubricate the Z axis leadscrew, and make sure the self-aligning bearings are not binding. They often do. There are numerous Thing-o-Matic modifications at thingiverse.com aimed at addressing this common problem. Worse comes to worst, you can reduce the maximum feedrate for the Z axis via your slicer.
On Cupcakes, this usually occurs when printing from an SD card. Owing to an esoteric reason, the first motion command for a print file from an SD card is run without acceleration. To confirm if this is the issue, try the same print over USB. If printing over USB resolves the issue, then you can either reduce the maximum Z feedrate or change your start gcode to not “recall home positions” and to instead assert them with a G92 command. For further information on why the first motion command is not accelerated when printing from a file, see Section 9.4.
Use ReplicatorG’s “Onboard Preferences” window to enable “Extruder Hold”. It is in the “Misc” tab. For extruders with high internal pressure — 3 mm extruders, typically — it is helpful to ignore gcode commands to temporarily disable the extruder stepper motor during a build. While this may not have been a problem for you previously, Skeinforge 50 generates these commands before any travel move.
Your extruder stepper motor may be turning the wrong direction. This is especially true if you just switched from RPM-based gcode to Volumetric 5D gcode. Try inverting the “A axis” from ReplicatorG’s “Onboard Preferences” window found under the “Machine” menu item. You will first need to connect your printer to ReplicatorG over USB.
There is a known bug in the Gen 4 electronics’ Extruder Controller firmware. That bug can be triggered by using an incorrectly configured “Altshell” plugin with Skeinforge. If you are using Gen 4 electronics — a Thing-o-Matic — and the Altshell plugin, then make sure that the “Use M320/M321” box is checked in the Altshell plugin’s configuration.
Note that the firmware on the Extruder Controller is not Sailfish. The Extruder Controller has its own firmware. The last release of that firmware was version 3.1 back in 2011.
If you are not using Gen 4 electronics or not using the Altshell plugin, then check the gcode in your print file.