I get the same thing on my Fox float/FSRXC. I've removed the shock to clean and grease the pivot points, and investigate the knocking. As far as I can tell, the source of my noise is that the bolt that secures the shock, which is also the pivot bolt, is just a slightly smaller diameter than the mounting hole on the shock arm(actually the metal bushing that resides in the mounting hole). This difference in size allows the shock to move around on the bolt causing the knocking sound. This is confirmed when I put my hand on the shock pivot point, lift up on the saddle, and feel the shock arm move(not pivot) and "knock" on it's pivot bolt. Either the bolt diameter is too small, or the pivot bushing inner diameter is too large.

Short of finding a slightly larger diameter bolt, or a bushing with a slightly smaller inner diameter, I can't think of anything else that would get rid of the knocking. If the bolt is the part out of spec, then replacing the shock wouldn't do any good, and I'm not willing to buy a new shock to see if the new bushing fits better(only to find out it's the bolt's fault after all).

Sucks...