Java – Why is Eclipse Platform Dependent?

Java does a very good job on isolating you from the underlying OS and gives you the same exact tools on most platforms it works on to talk to things in the underlying OS.

Python on the other hand does not do as good of a job in isolating you from the underlying OS, It does not have a standard way of handling between process communications (look at the differences in the sys module and os module between a windows and *nix implementation of Python for example.)

I have written code in python that would only work on a *NIX box or Windows box using just Python available API calls, where in Java it would be very difficult to write code that was just Java API that would not work the same on both a Windows box or *NIX box

I think the main reason is that BlueJ runs your code in a VM with a debugger attached. BlueJ actually has two VMs running: the main one, and the one with your code inside (the user VM, aka the debug VM). The main VM has a debugger attached to the user VM, which allows it to do things like pause user code, inspect the state of objects and all sorts. I imagine this probably adds a fair bit of overhead (perhaps inhibiting the JIT compilation?); the speed that code executes is not a major concern for a learning environment like BlueJ, as long as it's reasonable.