Ever consider the security concern of being able to automate IE for uploading files via a scripting operation? They did and that is why you can't set it from code. They don't want the responsibility for malicious use.

If you want to upload a file reliably check out another solution for file uploading. One such solution is from my company and its called HTTP Wizard SSL v2.

http://www.seekfordsolutions.com/products/httpwizard/

Good luck with your project.