I'm not positive this is the case, but this is how I see it: The most likely cause I think could be that the file upload process is a separate thread to the web server. If that's the case, then the load balancer would get the initial web request, which it's routing to HTTP. The file upload request, is generated by the web server to itself, which is not going through the load balancer, but rather resolving on the machine, and most likely, staying on HTTPs. Your browser is then getting 2 responses, one from the web server for the initial request, and one for the file upload.
I suspect that these have different headers because of how the load balancer is manipulating the request from HTTPS to HTTP, and that is where the issue is. Anytime your browsers receives content from mixed protocols (HTTPS + HTTP), it will warn you because that is a very common phishing attack that hackers will use.
I would think the simplest solution would be to configure the IIS server for HTTPS and test.