When you use the 'Go To Related Record' step and specify that is should open in a new window, the 'OnWindowOpen' script trigger doesn't fire. (The 'OnWindowOpen' trigger is defined at the file level.)
Product and version ( FMPA 14.0.3, FMPA 13.05)
OS and version: OSX 10.9.5
Workaround (if any): manually define a script call after the GTRR that calls the same script as defined in 'OnWindowOpen'
I have spoken with other developers who say they also see this behavior.