do you use Eclipse as your AUT and test a plugin you are developing? What are you trying to export: a Jubula project, test results, ...? What plugins did you install (the Eclipse you´re writing tests with and your AUT)? What is the error message? The more information you provide the easier it is to help you solving your issue.
Can you provide the log entry that occurred at the time when you tried to export?
Can you reproduce the behaviour after a restart of Jubula?
Without knowing more, I can't say whether the problem is due to the H2 database, but we do not recommend using it for productive testing.