You are most certainly using @Html.Raw(Model.MainBody), instead you should use @Html.PropertyFor(x => Model.MainBody)

cheers!

Neary true Marcus,  I have a helperfunction 

@helper NavigationItemTemplate(string header, XhtmlString content) {

    <div>

    @if (header != null && content != null)

    {   

        <h3>@header</h3>

        @content

    }

    </div>

}

And when writing @content it does this.
Using ProprtyFor fix this

There is another solution to this problem that we find and I write it here so others can use it.

There are places where you can't/don't want to use PropertyFor, for example in the footer of the page or in a more advanced menu. In that case you can use @Html.XhtmlString(content) (Where content is XHTML-string) instead of just @content and that will make EPiServer to write out friendly url instead of unFriendly.

Thanks to Magnus Forsberg at Active Solution who showed me that