Hmm, I was unable to reproduce your results on my first attempt. Here's what I got: https://gist.github.com/bd3d716fbd30569dbe42
The first two results are JRuby master on Java 6 and Java 7, respectively. The Java 7 run is faster...not by a lot, but definitely faster.
The third result is JRuby master on Java 7, but with invokedynamic use disabled. You can see performance drops off measurably, settling in closer to the Java 6 numbers.
The fourth result is JRuby master on Java 7, using invokedynamic, but forcing all files to compile on load. These numbers are the best of all, beating the Java 6 numbers by a solid 20-25%.
Try reproducing these numbers again with current JRuby master and 7u2.
If you are still seeing Java 7 perform worse than Java 6, we'll start to turn on some logging flags to investigate. I suspect it may be a combination of things...native and VM memory overhead (overall CPU use is quite low), lazy compilation confusing the JVM JIT (-X+C helps that), and perhaps other peculiarities in your code or in the libraries that sometimes manifest as slow perf and sometimes do not.
I will also note it is a very noisy benchmark. Under such circumstances, the usual problem is memory-related.