I got stuck on this kind of issue for a long time : all upload working fine except using IE using flash and https.
In fact the issue was strangly on server side, I was using commons-fileupload from apache to handle my upload java side. It was in version 1.2. Switching to 1.3 has fix my issue. It has a bug reading the file size.
This is a bit old but I'll reply anyway for other people.
Adobe Flash uses the Operating Systems certificate store to validate certificates for https on the client machine when using filereference upload. Internet Explorer also does this, so it works with Internet Explorer. However the other browsers use their own certificate store to validate https certificates so it fails on the other browsers. The way around it is for the user to install the root and intermediate certificates in the browser certificate store of your https certificate. I ended up providing a link to the root and intermediate certs and instructions on how to install for the users. A less than ideal solution.
We are slowly moving away from Flash on the web site, but it will be a couple of more years before we can rewrite this portion of the web site. It s apparent that Adobe is either unable or unwilling to do anything with this issue.