I've used Ninjas for the last few years and loved the sink. It worked great on 45 to 90 watt CPUs and ran super quiet. I started to notice on the upper end dual core CPUs that push 90+ watts that the thermals would rise after a few minutes of heavy crunching. I didn't worry about it until I got a CPU that ran into the 100 to 120 watt range. This really became a problem with the Phenoms where the Ninja 1100 would not perform any better than the stock 4 pipe sink on the 9850BE Phenom. I examined the Ninjas thermal interface plate and heat pipes.
First the heatpipes because they were close together causes a little problem with heat dissipation to the AL plates. This is now changed to match the Mini with the newer spaced pipes. Problem solved (Cool).
The second issue deals with getting the heat from the CPU/Hear spreader to the pipes. On the 1000 and 1100 series I have, contact with the lower heatpipes is not that great which may be an issue. The upper headpipes have even less contact and heat has to transfer though minimal contact with the lower pipes as they cross. The only other contact is trough the metal plate/sink about the pipes but that heat has to conduct a longer distance. This is where a huge performance loss occurs because it takes time for heat to conduct. The longer the distance, the slower the conduction which means more heat builds up at the source waiting for it to conduct away. That said, the upper heatpipes are only secondary dissipation and carry a much smaller percentage of the heat load.
What I would like to see Scythe do it change the interface plate a design where the pipes sit in channels allowing the more contact with the pipe. current contact is about 35%. With channels in the plate, you would see 50% to 95% depending on design.