It is highly unlikely that having iWork '06 along with iWork '08 causes problems. The only thing they share on my Macs are the templates in My Templates. Pages 2 will give me an error when trying to open any of my templates that have been created with Pages 3, which is to be expected. I've even had them both running at the same time when searching for answers to posts here.
Take a look inside the Pages 3 application package & see what's there. Go to HD > Applications > iWork '08 & Control- or right-click on the Pages application & select Show Package Contents from the contextual menu. In the new window that opens, open Contents > Resources > Templates > Business Cards. How many are there? As it is extremely difficult to accidentally delete any of the built-in templates, the problem could be a corrupt plist. Quit Pages & go to HD > Users (your account) > Library > Preferences & delete the com.apple.iWork.Pages.plist, empty the Trash & restart Pages.
