Secure/nonsecure messages in MovableType 4.2

I have been lately working with a Movable Type install on an SSL-enabled server. In IE, I keep getting pesky warning messages:

This page contains both secure and nonsecure items. Do you want to display the nonsecure items?

I disabled Javascript and the error messages are gone, so I figured the culprit must lie somewhere in the Javascript. One particular file, JavaScriptFlashGateway.js, contained
flashTag += 'codebase="http://download.macromedia.com ... ';

I’m going to see if updating that will address the issue, but I have a feeling there may be other issues. Has anyone else run into this? My Google searches have been coming up empty.