Java Interface issue that makes no sense to me

There's a Java tool I have to use, called Blast2GO. It's a Genomics thing and I'm very sure that program itself is not the problem, but it is the only reason I'm using Java. We run this on data wholesale, so we're waiting with bated breath for them to release a command-line interface or API for it, but until then, there's the GUI. And if you're repeating a GUI interface a couple dozen times in a row (easily), it becomes more and more likely that you'll forget something.

So, we're trying to automate it. We're using Sikuli. In a way, Sikuli is a wonder. It uses computer vision libraries to find and click things in a GUI environment. It has allowed us to automate much of the interface, which is a wonder.

In another way, it's totally wrong. GUIs are not a pipeable environment, and if you're going to automate something, command-line scripting is the simplest way. Stupid interface issues pop up rarely that way, while my wrangling with Sikuli is all about handling stupid interface issues.

And the most stupid, the most unsolvable stupid interface issue is this: I run Blast2GO on a Solaris server because that's where the data lives. So, I use X Windows to redirect the output onto my local machine. And right now, wherever I run it from, I lose the ability to navigate menus via arrow keys and move through open and save windows via tab. And, for the life of me, I have no idea why. But whenever I run it on those servers, I can't use those keys. This makes the scripting much harder.

Any idea why Java would be doing this to me? Is it a Solaris issue? A Java issue? An X Windows issue? Help!