We had trouble using the HTML5 with EPiServer CMS, it proved to be a bug.

The bug is that you have to write html 5 doctype in uppercase, ie <! DOCTYPEhtml>, to write doctype in lowercase makes EPiServer html parser removes thedoctype.

The actual bug is that the doctype should be case-insensitive - that you can see if you read the documentation for the doctype.

so use the <! DOCTYPE html> until the bug is resolved.