When using Shadowbox with links in excerpts I found that the rel attribute is not closing properly, the last " misses. This causes the rel attribute to be filled with text from other excerpts, causing a really long link. (with shadowbox still working though, just some posts missing in the rel attribute).
After a quick look in the code I guess this is because the rel attribute was not originally there, but i'm not sure. I fixed this manually by adding the " in the frontend.php file but i'm sure you'll have a better idea.
I'm not sure if there are others with this problem, didn't seem to find any questions regarding this. Just thought I should let you know!