Do you play in English?
I believe that the official answer is, "Nobody knows". At least, Cycrow has said that he does not know, and I do not know.
Names are determined by language files. The game should, theoretically, use the name listed in the highest-numbered language file for that name and language. The "ZM_EMP_BLANK_WARE_CUSTOM16_13" should be in the lowest-numbered language file for that name and the English language, at least. Other languages may also be supported. That means that the correct name should always override the ZM_EMP name. Emphasis on "SHOULD".
See
Language Files: How to modify for your language for more information about language files.
Sometimes, though, the game does not seem to read the correct name. This is that part that I have never seen explained. In my experience, the game will USUALLY find the correct name after a few seconds. However, this is not ALWAYS true.
If the name works correctly sometimes, then you probably have the script installed correctly, and your language is probably supported.
Another possible reason can be when one file of a multi-part script has not been re-compiled after a change in the name. However, Improved Boarding only uses the name in the setup script to install wares at certain equipment docks. So this is unlikely to be the cause of the issue that you report.
Bottom Line is that it happens sometimes. AFAIK, nobody knows why. Sorry!