Gunnar Langemark has been highlighting numerous web sites that are published using Drupal, an open source content management system and community platform. If you are researching Drupal, you should review the sites that Gunnar has highlighted. Really impressive stuff.
This kind of split is one of the risks of open source projects. I think it can also be a healthy, long-term, survival mechanism as well although it certainly adds some chaos in the short run.
This thread has the answer to why a pop-up window suddently began to appear when I booted up my Windows XP box at home. I had installed Apache and a demo of the Zend PHP editor. The pop-up error began once the demo license expired yet it gave no indication of what system was causing the error. I thought I had gotten infested with a virus until a little googling turned up that thread above. Zend needs to improve that error to something meaningful.