I started a site using phpBB3. I had no real issues with it, but I came to a point where I wanted the site to be more "mine", instead of using other people's work. I also ran into a wall in terms of overall design continuity and integration. Even finding a good looking skin for phpBB isn't enough to really make it match perfectly with the rest of your site. I still liked their account system so I re-wrote the forums from scratch, using the phpBB account system. (BIG MISTAKE)

Then later on, I decided that I wanted to completely abandon phpBB.

To be honest, I really believe that if you want to make a site that (you hope) will become popular, using a template such as phpBB or vBulletin just isn't professional enough to get the job done.

In fact, I'm quite surprised that a huge site like SitePoint hasn't created their own message boards, however I'm almost positive that this relates more to the sheer amount of users that are already signed up on the current ones that it doesn't make much sense for them to re-do their entire system.

***EDIT*** A major reason I switched to my own system was to avoid all of the bells and whistles that come along with templates. I have no real need for signatures, 10000000 different permissions etc..