Here's some things to try (if you haven't already)

1.) Ensure Java heap size is increased (-Xmx256m ?)
2.) During imports:
SET LOG 0;
SET CACHE_SIZE 200000;
SET LOCK_MODE 0;
SET UNDO_LOG 0;
3.) Experiment with the nio option in the URL
( jdbc:h2:nio:~dbnamehere )
4.) If your data has very large columns, it could be triggering CLOB
handling, which would slow things down

More details on peformance tuning at:
http://www.h2database.com/html/performance.html#fast_import

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