I am having similar issues. I would greatly appreciate any help. I click on my Help element with IE and Chrome Driver and the Help dialog pops-up just fine. With Phantom, I do not believe it is popping up, yet the click on Help does not indicate error.
I wrote in another forum and attached pictures:
PhantomJS Driver in Selenium/C# Test not seeing/clicking items or modal popups where IEDriver and ChromeDriver do.