Content Query Webpart breaking html

Hi,

We are trying to use the content query web part to display content from a document library in a site upgraded from sp 2010 to sp 2013. However, it seems the content query is breaking the html in our custom master page i.e. it seems to be removing the following line "<div class="clr nf"></div>", which is causing the background colour to merge into the content area. Any ideas of how I can avoid or get around this issue?

thanks,

Sherazad

Sherazad