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http://forums.textpad.com/viewtopic.php?t=10233
Here i posted some info that will answer your question.

Previously I explained the way you can get around the problem that I figured out by limited knowledge and messing. I now just found out that you can make the Tool output in a Command Prompt window unlike i said earlier. To do this all you need to do is un check the Capture output checkbox, and now ...

For those that are having the same problem and still want to use this GUI. Here is a solution that takes about 2 seconds longer than if you could use the Tool: Go to the Tools menu, and select Run... Make sure the dos command checkbox is selected, and then type "java"(without quotations) in the ...

Oddly enough, I have Java SDK 6.* installed yet the tools were not automatically found. I manually added these two tools, seperately, namely used Add > Program and then searched for javac and java and added them. The Compile tool works, but the Run tool does not. I think I know why but im not 100 ...