I had that problem today, and I might be able to help you.
Open your project and run the script again. When the "Script failed" and "TOC file found" messages appear, close them. Then open the Output View pod, and look for the following message at the bottom. (The "massage" typo is not from me!)
Batch generating layout "WebHelp"....
Error: Closing MessageBox with massage "Please select a new project subfolder, or a folder outside of the project path." and type="48".
The message means you need a separate project folder in which to save your Eclipse output.
Once this happened to me, I created a new folder called Eclipse on my computer's desktop. Then I reran the Eclipse Generator script. When I was prompted for the help output location, I browsed to the new Eclipse folder on my computer's desktop. That time, it worked.
Thank you for your response but the issue for me is different. I’m running a customized script that Adobe wrote specifically for our company years back. The script has been altered several times by a developer here and he’s too busy to help me right now. Things will calm down soon and he’ll have time to help me again. For now, I’ll have to live with an ugly workaround. (But it’s a lot prettier than editing lines of xml code by hand!)