After isolating everything in Java (including ditching the JDBC driver for lower-level SQLite bindings), nothing changed. It was likely JNI overhead, but frankly, that doesn't matter: Java was too slow. No sophisticated benchmarks here — just real-life production code that runs like molasses in the JVM and runs acceptably in C++.
Also, C++11 is not a low-level language anymore. (And I say this as a long-time Lisp and Clojure programmer.)