Its possible. Google certainly throws pagerank away when they encounter a nofollow or a link to something that can't be crawled because of robots.txt.
In the end, it shouldn't matter. Based on my observations, Google has changed their algorithm to differentiate between internal and external pagerank. Within your site, they use internal links to calculate an internal rank for your pages. So if you throw PR away somehow, these internal ranks will be lower. But then it appears that they calculate a separate domain rank for your site and scale your internal rank to your domain rank. So if you throw away a lot of PR, it only changes which pages on your site are ranked highly, not by how high they are ranked.
If they were somehow counting ads as external links and decreasing your domain rank because of it, that could hurt you.