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Yeah, I'd say you need to wait and see now, since you've added a different type of link (text, absolute link rather than a relative one as is used in the logo). The home page links using the logo are fairly buried in the body of the HTML but that really shouldn't make a difference to whether WMT picks them up, unless I am missing something.

It finally updated. The update ran parallel to Google's caching schedule and all the stuff I did in webmaster tools as well as linking/pinging/etc... didn't have any affect. Google's a just a fat donkey... you can crack the whip all day long but that ass ain't gonna move till it's ready to.

Hey! You can look into the software WebMeUp for tracking rankings through projects/URLs and lots of keywords. I'm using Moz, OSE and WebMeUp for various reporting and monitoring. You may find it useful for this particular task or something else as I have. Cheers! - Patrick