You know, I think it's a combination of clock speeds, hard drive speed, RAM speed and probably the in/efficiency of the code behind the software.
With the Boxx configurations I'm looking at, all of those are greatly improved. We'll see though. I'm not a huge fan of benchmarking. I just need to load up some of my known, problematic projects and see how they behave in AE and C4D.
Thinking a Titan and much higher clock speeds should really help the most.
I actually started to window shop around the BOXX website after I replied to your post (sacrilege). A chat window popped up on the site and I ended up having a brief conversation about my Mac Pro frustrations (especially after I saw all the hardware options on the BOXX website . . . liquid cooling?). He even offered a 5% discount to switch to one of their systems, so you might want to bargain with them a bit if you decide to go through with it. Either way, even though this is a "Mac Pro" forum, you definitely have to follow up and let us know the details of the BOXX setup and how it compares to your previous Mac Pro experience.