Perhaps you've done what I recently did... I thought I was highlighting away and went back a page to check something and nothing on the page was highlighted. Checking other previous pages revealed the same thing and I was a bit miffed! I found out I didn't really have the highlighter tool on, it was the text selection tool instead and it looked
exactly the same marking text. The easiest way to tell is in the top bar of the ereader, the highlighter tool should show a boxish marker on it to indicate it's selected.
