I had a similar problem exporting a CSV file from SSRS, where Excel would open the file as a single column. Turned out that the default SSRS export encoding for CSV was unicode, and Excel did not know how to handle that. I found the "Render" section in rsreportserver.config where you can override the encoding - set it to ASCII and that fixed my problem.

Not exactly the same as the OP's issue but hopefully this will help somebody.