We came to a conclusion in "The Editors" on this thread http://www.opserver.de/ubb7/ubbthreads.php?ubb=showflat&Number=425223#Post425223
that there is a bug in map_subents. In making my level, I have separate rooms that are placed from WED, and those rooms contain models. When loading the main level, the rooms load, but the models in the rooms do not. I have map_subents set to 1 right before the main level is loaded, however, it does not work.

Thanks for the report! Yes, that was a bug. It will be fixed in the next update.