I believe what you're seeing is a glitch that occurs when there is an unusually long, unbroken line of text in a thread title or private message title, or username. It stretches the forum width to accommodate, which runs it underneath the ad bar.
Agreed--it is annoying! It's something that's been brought to the attention of the developers in the past, but I'm not sure where in the queue it resides, as it's a sporadic issue and therefore is prioritized below things that need immediate repair.
It's admittedly not much help, but in the case of the main forum, I find the issue typically resolves fairly quickly when the odd thread is no longer on the page I'm viewing.
If people are having an issue with a popular thread repeatedly causing this problem, we'd actually be happy to go in and tweak a thread title to break up the characters if we're given a heads up.