The problem with Java was that it was impossible to get it running fast enough. You had 1 second of thinking time, but with Java you could barely access 0.05s, while compiled languages like C/C++ or even C# could easily use 0.95s without having any timeouts (which leads to disqualification).
My impression is that as long as you can ignore startup time, Java in general is pretty close to C++ and definitely much faster that Python. I am surprised this would be a problem with Java and not with Python. Did anyone had the same problem with Python?
The contest site had a problem with their JVM which interacted badly with their sandboxing environment. The 1-second time limit would disqualify any Java entry that took something like 50ms or more for some unknown reason.