CT2003 - Validation results different with differnt CT versions

I've verified this using a few versions of OpenCDISC and Pinncle21 versions.

When validating using the controlled terminology for file 2015-09-25 or earlier.  We receive many errors stating ....values do not have the same code in cdisc ct.If you run using any later version say 2016-06-30 we do not receive these errors.  we are not changing the transport files or another setting within the validator but the validation report does not show these errors.   I don't see any difference terminology files that would indicate why this would not report (other than the records for these items are further down in the file do to file changes that occurred during the December  2015 CT release).

Is there a change in how these rules are being evaluated or is there an issue with using the much longer CT files in processing the validation?