So I looked for the steps/mm setting in the firmware and couldn't find it. I tried forcing it with M92 X100 Y100 - no luck.
I tried loading the gcode into ReplicatorG and printing from there. Better, it printed 49mm. Still not really good enough. But it's weird that the same GCode would print differently.
Finally I looked into gpx.exe, and found that there was a s3g-decompiler python script. I ran that on the x3g file and examined the output, and discovered that apparently Makerbot's s3g/x3g files do the steps/mm calculations in the file generation, and the printer just moves the specified number of steps.
This seems pretty backward to me, it means that the x3g/s3g files are specific to a given printer. It's not really horrible but it's not what I'm used to.
So it turns out that I needed to create a custom machine configuration to get precise settings. The X/Y/Z are pretty easy, the extruder less so.
I started with a calculation, 16 tooth gears, 3200 step per revolution, 2mm belt pitch, should have resulted in exactly 100 steps per millimeter. But for some reason, it didn't work out.
I eventually used a dial indicator (I gotta get a new dial indicator - the one I have reads in inches. I never EVER want to read anything in inches) and wrote some quick GCode to home, then wait 10 seconds between moving to +10mm and 0 repeatedly. This allowed me to zero in to within about a hundredth of a millimeter.
I did similar for the Z axis, putting the dial indicator underneath.
For the extruder, I wrote some GCode to just heat up, wait 10 seconds, then extrude 100mm of filament. I marked with a sharpie up 100mm from the inlet of the extruder, then let it go. It came up a few mm short the first time, after some adjustments it was fine.
In the end I came up with a config file for this printer that results in good prints:
And here's the file:
Put this in your GPX directory, then when running GPX, use a command line like this:
(gpx directory)/gpx.exe -g -c (gpx directory)/CTC.ini (gcode file) (output x3g file)
Hope this is helpful.