SEOmoz posted results from a study he did where he concluded that only the first anchor text on a page is counted by Google as the anchor text for that link.
For example, let's say you have a two links to the same URL on the same page. The first link on that page uses the anchor text [Big Blue Pineapple Chair] but the second anchor text uses [Small Red Cantaloupe Chair]. Which one will Google count as the true anchor text to be associated to that page? According to Rand's study, it is the first, i.e. [Big Blue Pineapple Chair] and not the [Small Red Cantaloupe Chair].
The Sphinn thread on the topic actually says this study was first conducted by the SmackDown blog (here is the Sphinn thread for that post). Smackdown explains that you may want to rethink linking your logo to your home page if this is the case. I am not sure about that, unless you use some weird code that interprets the image tag as an anchor tag.
It makes sense why Google or any other search engine might pick the first use of anchor text for a page on the page. I personally did not validate the studies but it is important to point out, nevertheless.
There is also a debate about nofollowing those links and what type of impact that may have on those links.
Forum discussion at Sphinn.