Cache misses are a possibility; try the integer version with long, so the size of the data is the same as with double. The other possibility I'd consider likely is that the JDK you were using implements caching in Double.valueOf(double). This could be dealt with if Clojure boxing directly called new Double(double). Caching in valueOf methods has been known to cause trouble in other situations, involving Java, primitive boxing, and performance. Besides the caching wrecking memory access-pattern locality, causing CPU cache misses, it likely involves acquiring and releasing a global lock on the Double cache, which will kill multithreaded performance particularly.
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