Is your honeypot a hidden form element or an actual text input that is positioned off the page?
That may be the issue without knowing how you set the honeypot up. I know in the past, when I have used just a hidden form element for the honeypot with a blank value, it didn't work at all.
But, if you make a text input box and give it an id like "honey" and then add a class to it... call it .honey or whatever else. Then for the CSS in .honey, set the position to absolute and give it a left value of something like -9000px. That way, a bot will see it but a human won't. Then do your PHP check to make sure that $_POST['honey'] is empty or FALSE before letting the form continue to process.
Just some thoughts... sorry if I am telling you something you already know.