ACH file generation does not seem to match format requested

We are using Dynamics GP with multiple companies. Our EFT file format is set up for each company exactly the same way (I had copilot compare them), but when we generate an EFT file in one company it does not seem to follow the format requested. I even created a new format and there were no changes to the file generation. What else can I try to get the program to create the correct NACHA file?