Yes I just checked my extension I have the same issue. Looks like a bug to me. You could use message passing to the background page and then open the page from there. I have posted this suggestion to your question on stackoverflow.
One fix if you don't have too many links to open could be to send a message to the background page and then call a function from within the background page to open your window.
I checked and both and chrome.tabs.create and the standard javascript window.open will open an html file in the extension.