I found a problem using our own ilastik plugin for imagej :o and I have zero clue how this is caused.
But first the symptom:
When running pixel classification with macro recording turned on, and selecting probabilities as the output type the macro recorder correctly records all parameters (that have a label in the relevant code):
Hm, that’s interesting. The only cases I know where commands are recorded without the option string are caused by premature triggering of the recorder due to the use of IJ.run() in plugins, see these related discussions:
But all these are specific to ImageJ1, and as far as I can see, your plugin is exclusively using IJ2 functionality, so I assume your issue is unrelated.
When quickly reading through the code, it seems the code path for the two conditions, Probabilities and Segmentation, is quite similar, and mostly differing in this additional if clause:
So, without having tested anything: would it make a difference if you add quotes to the command line, in agreement with the ilastik documenation?