This was definitely not fixed in FileMaker Pro 12.0v2 unfortunately. There's an active issue report discussion over on the FMI Forums at:
which I've been following as I've also been badly affected by this bug. If you have a file that can reproduce the issue I'm sure FMI would be glad to receive it as that has been one of the problems so far in tracking down - being able to consitently reproduce the issue.
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Thanks for the update.
I can confirm that this bug also affects me. A lot.
I have noticed that is does not seem to occur in Runtimes bound with FMP12.
At least, it has not happened yet.
I am not sure why the New Window script step would execute differently.