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I'm surprised it works directly in the user interface but not in script mode since that is not the paradigm that FileMaker scripting works on. It may have to do with whether the other file is already opened. When I need to do things in another file, I open that file and then tell the first file's script to run a script in the newly opened file instead of trying to put it in the first file. It is weird to write a script to do things in a file that it is not in.
Of course, where possible, I try to combine files like these into a single file and you'll avoid that problem as well as many others such as security issues between different files.
If GTRR doesn't work, just manually do it. Set a variable, go to the new file, enter find with the variable and you should have what you want. While GTRR should work, I would not spend hours trying to figure out why when there is an easy work around. That is unless this is more of for the principal of the situation and no one is paying for time on it. But that is up to you. If you have a sample of these files you could upload, I bet we could figure it out because GTRR should work.
Best of luck!