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Hmm... the "of machine" text is meant for those uber-geeks who are running their web server and ACGI script on a different machine than their copy of OmniFocus. For example, I do it because I use a MacBook Pro, and ACGI Dispatcher is not a Universal app. I'm not sure how commenting out this line would have fixed things.

However, with respect to the timeouts, I think I know what's going on.

The ACGI Dispatcher needs files saved with the "Stay Open" option checked. When you save changes to the script, Script Editor will sometimes un-check this option. You can tell this is happening by watching your dock: if, when you load the page, the .acgi app closes immediately after it starts up, something's wrong.

Here are the hoops you need to jump through in order to get this to work:
  1. Open omnifocus.acgi in Script Editor, and select "Save As..." from the File menu. Check the "Stay Open" option, and save the file.
  2. No matter what you do, Script Editor will save the file with an ".app" extension, but ACGI Dispatcher needs it to be ".acgi". To get around this, find the file in Finder, press Command-I to Get Info, and under "Name & Extension," change "omnifocus.app" to "omnifocus.acgi". Click the "Use .acgi" button when it asks you to confirm.
  3. Now, go into Script Editor and save your document again. It will warn you that "This document has been renamed to "omnifocus.acgi'." Click "Save" to save the document under the new name.

You can now hack away at the script:
  1. Make a change to the script
  2. Save the script
  3. Close the running copy of omnifocus.acgi
  4. Re-load the script in your browser
  5. Repeat

With respect to your original error, I have no idea. I have no way to reproduce the issue on my system, and I don't have the time to offer "official" support. Hopefully, this will set the stage for you to fix the problem yourself; if you find a solution, please share.

Best of luck,
-d.