Why doesn’t Internet Explorer 11 honour conditional comments even when emulating Internet Explorer 8 document mode

I wouldn't do it. Use virtual PCs instead. It might take a little setup, but you'll thank yourself in the long run. In my experience, you can't really get them cleanly installed side by side and unless they are standalone installs you can't really verify that it is 100% true-to-browser rendering.

Update: Looks like one of the better ways to accomplish this (if running Windows 7) is using Windows XP mode to set up multiple virtual machines: Testing Multiple Versions of IE on one PC at the IEBlog.

Update 2: (11/2014) There are new solutions since this was last updated. Microsoft now provides VMs for any environment to test multiple versions of IE: Modern.IE

It sounds like you might have some debugging code in your javascript.

The experience you're describing is typical of code which contain console.log() or any of the other console functionality.

The console object is only activated when the Dev Toolbar is opened. Prior to that, calling the console object will result in it being reported as undefined. After the toolbar has been opened, the console will exist (even if the toolbar is subsequently closed), so your console calls will then work.

There are a few solutions to this:

The most obvious one is to go through your code removing references to console. You shouldn't be leaving stuff like that in production code anyway.

If you want to keep the console references, you could wrap them in an if() statement, or some other conditional which checks whether the console object exists before trying to call it.