Couldn't you solve this by tracking the version of Java (for example) used initially to develop the simulation?
Philip Guo (pgbovine) addressed many of these problems in his thesis work, on Burrito (http://www.pgbovine.net/burrito.html ) and CDE (http://www.pgbovine.net/cde.html ). Both of these look very cool, but I've never managed to get over the hump and actually start playing with them.
At this point I should note that I'm actually in favor of fixing a bad standard-library PRNG---I just think it's important to understand (a) what could break, and (b) why users might be unhappy about the breakage. This isn't quite a Chesterton's Fence sort of situation, but it's similar in spirit.