I have just integrated my design built using twitter bootstrap, html5, css, jquery with dotnetnuke to create a skin.
The html version in on following URL: http://www.siddharthkpandey.co.uk/design/homepage.html, http://www.siddharthkpandey.co.uk/design/general2.html
The Dotnetnuke version is on following URL: http://www.siddharthkpandey.co.uk/museum/newdesign.aspx and http://www.siddharthkpandey.co.uk/museum/newdesign/generalpage.aspx
Both the versions works fine with Chrome, Safari and Firefox latest versions. The HTML version also works on IEs but I am not able to figure out what is the problem with the Dotnetnuke version on IEs!
Your problem is that you dont have the correct doctype. Copy one of the .doctype.xml files from the default darknight skin rename this to match the names of your skins example skin.doctype.xml and the refresh your page and it will look correct