This was affecting our QA team today and thanks to this post I figured a solution for the problem:
- In IE double click the "Certificate Error" icon
- Pick Install Certificate. Pick the defaults and finish
For some people this was not working still so I suggested to restart browsers and even Windows, you know that kind of stuff you need to do when suspicious right? At least one of my team members reported cleaning cookies resolved the problem for him (of course after following the above steps)
So SSL support based on self-signed certificates is buggy in flash and you can expect the same for SWFUpload. Look for SSL in the Known issues page for a similar statement.