<<I confirm that the Excel file automatically starts even if launched
through IE.

Assuming that the "export to CSV" function in your in-house web application
actually saves the CSV file to disk, then you may have an incorrect setup
in Explorer (regular file Explorer, not IE).

You might try this:

1. Start up (file) Explorer.
2. Click on Tools|Options.
3. Click on the "File Types" tab.
4. Scroll down the list to the CSV extension.
5. If it says that it opens with IE, then I would try changing it to
"Microsoft Excel Comma Separated Values File" that opens with Microsoft
Excel for Windows. The parameters for the Open and Print actions should be
similar to those of a regular XLS file.

--
Regards,
Bill Renaud