SYMPTOM:
Report Services Documents exported to Flash from Strategy Web are being exported to .mht format although the Project Configuration > Project Definition > Export Settings > Export to Flash file format option is set to PDF.
CAUSE:
A possible cause of the issue is that th Web Server wasn't restarted after the setting was changed; every time this option is changed under the Project Configuration, Strategy displays a warning message informing that the new configuration will take place only after re-starting the Web Server connected to that project as the image below:

Sample Code/Error
If there is a Web Server connected to this project, the changes for the following section(s) will be applied when it is re-started: Export to Flash file format