Seeing the actual scripts involved would be helpful.
I'm wondering if:
The second file has an OnFirstWindowOpen trigger set in File Options.
Also wondering if the script in File 2 needs to have a Select WIndow [Current Window] step added.
Also wondering if your file or a layout or a script might be damaged. Have you tried recovering the file?
Haven't tried recovery; will look into that. Good point about the file open options, will give it a look. If those don't fruition, will post some code.
Ah, appears that there was a script triggering onfirstlayoutopen. Thanks for the pointer, Phil.