HyperSQL Database Engine

I think the most likely cause is that Hibernate is not closing all database connections. Depending on how you are configuring Hibernate, the connection pooler will allocate a connection for data pooling control purposes, and I find that it doesn't close that connection. The HSQLDB shutdown property only takes effective when the LAST connection is closed, so in this case it will never run.

A work-around is to set WRITE_DELAY as Fred suggested.