Yeah, it's a bug with the extension API for extensions that replace the New Tab page. I was having the same problem. As far as I know, the only workaround is to modify the extension to open the clicked link in a new tab then close the current one. Chrome will then switch to the newly opened tab. I had to switch from using links to using JavaScript to accomplish this. Here's some sample code if you decide to try and modify Speed Dial...
Code:
function openURL(url1) {
window.close();
chrome.tabs.create({url:url1,selected:true})
}
Code:
<a onClick="openURL('SITE_URL_TO_OPEN');">URL TITLE</a>
Problem is if there's no HREF, then browsers don't treat it as a link. So play around. This is just how I do it. I just add CSS to make it have a Hand cursor so it at least gives visual notification of being a link. Also, it won't show the URL in the status bar either. I guess you could get around this by actually making it a link AND opening it in another tab AND closing the original.
Silly workaround for a bug.
Worse part is I won't even know if and when it is fixed.