Right blocks pushed beyond the header boundary

In certain cases, the right side contents are pushed out of synch with the header box. After some testing, I concluded that this is caused by the content overflow not handled by the base module (somewhere), that whenever the contents are bigger than it can be handled it pushes the whole right side out further. The problem would be corrected if the screen area is enlarged (by bringing the resolution higher). However, whenever the screen size is smaller than required, the overflow is caused (I tested it under 1200x1024 and the problem disappears but it is persistent at 1024x768). I am thinking it could be handled if the contents are regulated into certain size, but not sure how to approach. I think I saw some of the issues addressed in various theme section, but this is really the Drupal's short coming and theme design has little to prevent this problem. It would be really nice if someone who is familiar with the Drupal system to come up with some answers.