Do you have any idea about this?
Only a couple of guesses. . .
Is there something that has to be recalled for the slower runs?
Can you determine if the same sequence of events happens in both cases (i don't have access to any java, so i have not done any of this kind of testing). Do both runs require the same memory and i/o?
Are there any client configurations that have (or should have) changed between 1.4 and 1.6?