Nothing random about it, its basically caused by a hack the CSS in that book uses that breaks when font sizes are rescaled. You can either disable font size rescaling in the conversion or open up the book with the calibre editor and edit epub.css removing the rule:
Code:
/* fix for double-digit code listing numbers */
#conceptual_flow_with_tasks .code-lines li:nth-child(n+10) {
text-indent: -6.55em;
}
Basically the CSS in that book uses a mixture of rem and em units for different things, that does not play well with font size rescaling.