Okay, weird thing keeps happening. When I have the scriptographer window open it doesn't really matter which field I am in typing in a new value, it can be in the transform window, setting a new stroke or changing the size of type, whenever I hit enter Windows (or more accurately explorer) wants to open up the .js file, regardless which script I have selected but only after it has been run once and still remains selected in the palette. It doesn't matter if the script windows are still up or if I have closed them.
Deselecting the scripts completely, or shutting the scriptographer window, solves the issue.
Adobe Photoshop CS4 running under XP, service pack 3.