Command-Line Validator - CT Rules Not Triggering

On one study we're working on, a co-worker noticed that there were more issues showing up when OpenCDISC 2.0 was run interactively than when it was run from the command line.  Looking closely at the results, it appears that the command-line invocation of the validator did not use the controlled terminology rules with OpenCDISC IDs of CT2001, CT2002, CT2004, and CT2005.  (These were the only CT rules triggered by the data--CT2003 and CT2006 appeared in neither report.)

In both cases, the configuration file used was SDTM 3.1.3 (FDA).xml from the OpenCDISC Community download.

Are there any suggestions of things we might look at to determine why the command-line invocation is not finding issues for these rules?