There are known large-file support bugs under JNI in various releases of the JDK. Please upgrade to the latest release of the JDK, and, if that does not solve the problem, disable big file support using the --disable-largefile configuration option.
The Berkeley DB Java code checks a system property for the library name before defaulting to the released library. On Windows, run as follows (note the 'd' at the end):
% java -Dsleepycat.db.libname=libdb_java-VERSIONd
On UNIX, try:
% java -Dsleepycat.db.libname=db_java_g-VERSION
Copyright Sleepycat Software