I decided to write a small post on this, this it has bothered me since I installed Komodo 5.
I had written a perl script and was trying to execute it, but every time I did, the Komodo IDE would pop up a Debugging Options window. I am new to both Perl and Komodo, so I didn't feel I had any use for debugging arguments and when I closed the window, Komodo would stop executing my script.
It turns out the fix is simple. In Komodo you go to the main menu at the top of the IDE, choose -> Edit -> Preferences... At this point the preferences windows is displayed. Now choose Debugging from the Category list on the left, then check the checkbox on the right that says "Skip debugging options dialog (use Ctrl key to override)".
That should do it. Other people have had different problems, and unfortunatly I can only blog about the ones I run into.