It's always a good idea to have a "G92 E0" statement at the front of your gcode. You can get this in skeinforge through the start alteration file. This command resets the E axis. Basically what it tells the firmware is "Whatever your current position is - consider that to be 0". That way your first extrude command will be relative to 0 which is probably what you want.
Without this command, the E axis will retain the value from whatever it was doing before - including manual extrusions.
I got burned by this very early on when I switched from Slic3r to skeinforge, except my retraction wasn't just an inch. It retracted at a relatively high speed for a good 15 seconds. It took quite a bit of effort to get the hobbed bolt cleaned out.