I think I have found the cause of this bug - the Gnome Dictionary plugin
When I upgraded to Jaunty the problem went away and the Run was being activated on script files.
I was happy and didn't know what fixed the problem.
Today I tried to find a meaning of a word in gnome-do. But there was no option. So I looked in the plugins and the gnome-dictionary wasn't enabled. So after enabling a few minutes later I tried to run a script file and it opened it in Gedit than running it. I nearly had a panic attack.
So I disabled the dictionary plugin and Gnome-Do went back to having Run for the script file.
I think I have found the cause of this bug - the Gnome Dictionary plugin
When I upgraded to Jaunty the problem went away and the Run was being activated on script files.
I was happy and didn't know what fixed the problem.
Today I tried to find a meaning of a word in gnome-do. But there was no option. So I looked in the plugins and the gnome-dictionary wasn't enabled. So after enabling a few minutes later I tried to run a script file and it opened it in Gedit than running it. I nearly had a panic attack.
So I disabled the dictionary plugin and Gnome-Do went back to having Run for the script file.
Please fix this bug.