Tested using v 3.0.2 and the most recent nightly JIST build (several updates to JIST CLI). The following three modules do not generate Slicer XML when called from cli as

java edu.jhu.ece.iacl.jist.cli.run [classname]

• de.mpg.cbs.jist.segmentation.JistSegmentationProbabilityExtraction - no class definition error. Exception in thread "main" java.lang.NoClassDefFoundError: de/mpg/cbs/jist/segmentation/JistSegmentationProbabilityExtraction (wrong name: de/mpg/cbs/jist/modules/JistSegmentationProbabilityExtraction.
• de.mpg.cbs.jist.surface.JistSurfaceMgdmRepresentation - no class definition error. Exception in thread "main" java.lang.NoClassDefFoundError: de/mpg/cbs/jist/surface/JistSurfaceMgdmRepresentation (wrong name: de/mpg/cbs/jist/modules/JistSurfaceMgdmRepresentation)
• de.mpg.cbs.jist.cortex.JistCortexFullCRUISE -invalid character in cli arg. cli Usage: edu.jhu.ece.iacl.jist.cli.run [classname] -help
  cli Usage: edu.jhu.ece.iacl.jist.cli.run [classname] [run options]
  cli PARSE Error: opt contains illegal character value '/'
  java.lang.IllegalArgumentException: opt contains illegal character value '/'
  at org.apache.commons.cli.OptionValidator.validateOption(OptionValidator.java:73)
  at org.apache.commons.cli.Option.(Option.java:123)
  at org.apache.commons.cli.Options.addOption(Options.java:131)
  at org.apache.commons.cli.Options.addOption(Options.java:114)
  at edu.jhu.ece.iacl.jist.cli.JistCLI.parseParamCollection(JistCLI.java:216)
  at edu.jhu.ece.iacl.jist.cli.JistCLI.parseParamCollection(JistCLI.java:221)
  at edu.jhu.ece.iacl.jist.cli.JistCLI.(JistCLI.java:95)
  at edu.jhu.ece.iacl.jist.cli.run.main(run.java:45)

I think (1) and (2) could are just an artifact of moving older package locations to newer locations? (3) is likely to having a "/" character within the first word of one of the input paramater (or output parameter) descriptions. All special characters will throw an error from the CLI when attempting to run but will run fine using the GUI.

Cheers,
Steve