I tried to set innerHTML on an element in firefox and it worked fine, tried it in IE and got unexpected errors with no obvious reason why.
For example if you try and
Have you tried setting innerText and/or textContent? Some nodes (like SCRIPT tags) won't behave as expected when you try to change their innerHTML in IE. More here about innerText versus textContent:
http://blog.coderlab.us/2006/04/18/the-textcontent-and-innertext-properties/