No, this really looks to me like the checkboxes are correct, and what is shown in the graphic is that the first 4 CPUs are actually all 8, and the last 4 are the extra "hyperthreading" threads. Where it says CPU 1 Thread A and Thread B, I think that is actually core 1 and 2.
Your own comments support that. You said when you disable hyper, you see CPUs 1,2,3 and 4. When you go to the checkboxes and disable the last 2 (7 & 8) CPU #4 disappears from the graph. That would support that all the hyper threads were already disabled, and you just turned off 2 cores which where being represented by CPU 4 Thread A and B.
It may be either the way it was programed for all processors before hyperthreading, or a error made. Try having hyperthreading on, and disable ONLY CPU 2. In the graph what happens? I would guess CPU 1 Thread B, and CPU 5 Thread B will stop.
Also when you say when running Maya it shows 3 CPUs with 2 threads and 2 with 1. Well if the above is true, then it means CPUs 3 to 8 have 1 thread, and CPU 1 and 2 have a second thread running. That makes absolute perfect sense.
Again, I'm speculating, but I really really really don't think you would get a 200% improvement with such a drop in clock-speed.
Look at this graph taken from "2009 Mac Pro in hand - unboxing etc.". The new 2.26 is not twice as fast as the old 2.66 octo. 16,615 (2.66) vs 18,088 (2.26). And with geekbench, 11397 (2.26) vs 8090 (2.8). You shouldn't be expecting 200%. You are getting 170% and that makes perfect sense considering the new architecture.