Could you give me a step by step way to reproduce this? Are you running model maker twice on the same label map volume or different ones? From the editor or the model maker module GUI? Generate all or specific labels?

Here is what happened:

-I run Model Maker on volume A
-For unknown reasons the file lives in /tmp
-Whenever I run Model Maker on any volume from the GUI the output matches the model in /tmp (I generated all labels, but anyways both A and B have only label 1)

I erased the model from /tmp and the issue was solved.

I'm able to see that the generated model files aren't getting deleted from /tmp. I ran ModelMaker once and produced
/tmp/Model_1_1.vtk
/tmp/Model_3_3.vtk
/tmp/Model_5_5.vtk
and ran it a second time, which created a new version of the file /tmp/Model_1_1.vtk with an updated file size and time stamp. It was loaded and displayed correctly on finish of the CLI.

The main bug from a developer point of view is that the temporary files are supposed to be deleted from /tmp unless the following code snippet is used in the python console:
slicer.modules.modelmaker.cliModuleLogic().DeleteTemporaryFilesOff()
I've used it before, but the fact that the .mrml file that's passed to the ModelMaker is deleted after being loaded into Slicer makes me think that it's not a saved setting (otherwise the .mrml would be left). But the CLI logic doesn't know about the model files, they're output by the ModelMaker and loaded from the .mrml file that's passed back.

I'm not sure why you're seeing a duplicate model being loaded on the second run. My first suggestion would be to open up the Advanced tab and click on the Debug checkbox to generate more output. My suspicion is that you've been able to write the .vtk file out to /tmp but that re-writing it is failing. Look for the string in the console output:
Writing model Model_1_1 to file /tmp/Model_1_1.vtk
and see if there's any error messages after it. Also examine the time stamp on the file to see if it's actually been updated.
There's also the "Save Intermediate Models" check box in the Model Maker Parameters tab, that will try to save out more versions of the models and might provide some clues as to what's going on.

I finally did see this behaviour, when investigating bug 2428, I'd loaded a scene file with greyscale and segmentation volumes as well as a left over model, and the model maker wrote it's first model into the poly data of the model from the original scene, and then as I played with the visibility toggles, I lost the other models that had originally been generated correctly.

Fix for bug 2428 also fixed this, please verify and close the bug when you get a chance.

Closing resolved issues that have not been updated in more than 3 months