What JBoss version and OS you use?
OS - Red Hat Enterprise Linux Server release 5.3 (Tikanga)
JBoss - 5.1.0.GA
AFAIK the calculation of nanos might be not exact depend on the OS and JVM :( , maybe you test it with a simple java program.
Sorry i did not get you on this, but both java client program and server is on same machine. So it should return same nanoTime.
I've test the 'communication overhead' simple by using a dummy SLSB and the client call it 1.000.* times (with one and more threads) to have an idea of the average.
Also the duration depends on the payload (size of method parameter and return values).
What was the performance you were getting?