We are using HSQLDB as the primary database in server mode for an open source project (a RSS feed reader, here https://github.com/sismics/reader\).
Sometimes, when no heavy task is performed on the database, the hsqldb-server process hangs and it takes 100% CPU. I've attached a jstack if it can helps you.
The database is quite big, around 500Mo. You can find the structure here : https://github.com/sismics/reader/blob/master/reader-core/src/main/resources/db/update/dbupdate-000-0.sql
Thank you for this great project :)