Nothing immediately comes to mind that you haven't already covered. I always make sure I have the correct version of Selenium, IEDriverServer.exe and Internet Explorer. Having the correct version of Selenium which goes with the correct version of IEDriverServer.exe might be an issue. If you are testing against IE11 make sure you have at least Selenium 2.44 or higher. Version 2.43 or 2.42 might work but I know for sure 2.44 works with IE11.
Are you launching the 32-bit version of IE11? I know on my current client they have two version of IE11 installed on Windows 7 but they messed with the image to make them both the 64-bit version of IE11. The 32-bit version of IEDriverServer.exe should work with 64-bit IE11 but that might be a factor.
Looking for differences is a good idea. I like the fact you recognize it works with Chrome but not IE. Talk to the developers and see if there is any difference in the libraries they are using between IE and Chrome. It has been a while since I've seen any "if IE then do X else do Y" type coding but you never know until you look.
That is all I have. See what other data you can dig out from the configuration.