Fist of all: Thank U Yoast for your amazing plugin!!
About this topic, I'm having the same exact trouble in both my websites.
Hope it will be fixed soon but in the meantime I found a "home-made fix" that works fine for me: When I inserted muy Google ID I added ?rel=author at the end (something like this: https://plus.google.com/xxxxxxxxxx?rel=author)
By doing this, although in the homepage the plugin shows the publisher meta Google finds the author link anyway. I tested with the Google's richsnippets tool and worked ok.
You can try this and check if it works properly for you using the http://www.google.com/webmasters/tools/richsnippets
Hope I was helpful and to hear from Yoast.