Lose relationships with client to server script

FileMaker 7 Server on Windows. Main file with multiple related tables with simple relationships based on single key per table. Solution works fine. Internal script imports records from Table A to Table B. Script works fine when run from within main file. Set up utility files on client computer to run various reporting sctipts within main file during night hours using vbs scripts to open utility files. Most scripts run without any problems, finding appropriate pathway to host file on server and running without problem or user intervention. One file however, call an external script in main file which imports records from Table B to Table A. I constantly get an error message saying that the main file cannot be found. Confusing part is that when writing script in utility file it finds the main file and script find. I have even created a File Reference under Define File Reference to make sure files can be connected. No amount of fiddling or coaxing during past three months has fixed problem. This is the final step in automating the solution. Any suggestions are welcome.