The production hive-site.xml could well contain settings that differ from the defaults in HiveConf.java. In our case, we introduced a custom ORC split-strategy, which we introduced as the site-wide default.
We noticed that during HCatInputFormat::getSplits(), if the user-script did not contain the setting, the site-wide default was ignored in favour of the HiveConf default. HCat would not convey hive-site settings to the input-format (or anywhere downstream).
The forthcoming patch fixes this problem.