If CSS is applied, the rID index is reset in the file document.xml.rels. Then There's two occurence of rID1.
After a look in the code, I understood the rID index is built with a static variable of the class createDocx. Then this variable is shared between all instances of createDocx. Unfortunatelly when you add HTML with CSS, the code uses the class HTML2DOCX that instanciate another createDocx (in fonctions HTML2DOCX::generateXML and HTML2DOCX::generateDOCX), . Then the rID index is reset and the produced document contains corrupted rID.