Found something very interesting. It took several hours to pin down the problem, but it had to do with a specific jar.
With this library loaded, Jabaco starts to compile, and actually generates a jar, but never finishes. The progress bar, that appears when Jabaco is generating a jar or exe, halts at around 60 percent, and you can see that it's stuck, even though you can still move around and use the menus.
When you look in the generated jar, it's missing several modules, including the main one.
The name of the jar that seems to cause this, is Joda Time, at
http://sourceforge.net/projects/joda-time/files/joda-time
I've been using Joda Convert, which depends on Joda time, and everything works fine, when it's run inside the ide. But as soon as you try to generate a standalone jar or exe, with joda time in there, the output jar is not runnable.
Joda time itself is very useful, but it looks like I'll have to scrap it.