It's funny you bring this up today because I was just taking a closer look at my Diskeeper 2009. I've had it since XP, and now running it 64bit in Windows 7 and I have to say I don't think I am going to continue using it.
I have it set to Auto so it defrags in the background, one of their claims to fame is how it only works when the system is idle, and uses such negligible resources to run, and I will give it that as it accomplishes this part well, but I don't think it has ever done a good job keeping the drives defragmented 'automatically'.
The point of 'auto' is to set and forget it, but occasionally when I do a manual 'analyze' it tells me the drive is defragmented and performance is 'degraded'
So I ask myself whats the point? I'm sure that windows defrag can do just as good a job or better when defragging manually.
edit: I just noticed in your post you state that the built in defrag runs automatically as well. I did not know this and am curious if this is true. If it were than I have serious issues knowing that 2 programs running in conjunction cannot keep my drives defragmented!