I'm afraid I haven't seen this sort of behavior before. It appears to be a problem with IE itself, from the sound of it, but it's hard to tell. Do you have a stack trace? It looks like this is when launching a new IE instance, but I'm not sure. Also, what version of IE? It's possible that upgrading may give you a more stable IE (or maybe even downgrading - one never knows with IE).
Switching to a different browser, real or fake, is indeed another possibliity - Vapir-Firefox is nice (I'm totally unbiased in saying that, to be sure). I'm not familiar with PhantomJS. There is a headless alternative on the Watir API (give or take), which is celerity. Other headless, javascript-capable drivers are envjs's headless browser, capybara-webkit, or others.