Are you exporting the list from the File / Export menu or from within the Print Physical Inventory Worksheet function? I would recommend doing it from the Print Physical Inventory process, because the file name (CSV or Excel) will get appended with the Location code (so you get 5 separate files) and you have more control over the items selected for exporting (can suppress inactive items or items not allowed at the location).
Maybe there is a problem with over-writing the existing CSV file. And I echo Bob's comments about the simpler path.
If the export template is defined to create a CSV file, it should not also simultaneously create an Excel file - and vice versa.
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Regards,
Softrak Tech Support