So, if I understand you correctly, everything is fine when using Hibernate proper i.e. your test case works as expected?

But with Hibernate inside GlassFish, you have the aforementioned error?

If so I suspect GlassFish is doing something wrong.

Could you create a minimal war project (preferably a Maven one) with only the necessary things to reproduce the issue on a recent GlassFish 5? I'll take a look at what is happening. Even if I don't find anything, it might be useful in the end to open a bug in the GlassFish bugtracker.

Thanks!