Yeah, must be the switching and splitting tasks.
That is very possible.
As I said in another thread the Core2 processor may be responding differently and setting the affinity manually is working better. AMD with the right fixes and drivers will do the 'splitting' correctly in 3D applications which is what their dual core optimizer driver was designed for.
I would still look at the processes being booted and run. Manually setting affinity may be having a positive outcome for some because they do not have their systems correctly optimized for performance and running processes/services that are not needed during FSX use. Switching the affinity may very well be allowing excessive processes to have the primary core and the game the other, eliminating the problem.
Bottom line is, if it works, thats all that matters. Setting affinity is easier than going through the system and cleaning out start keys and services that are not needed but still, the more resources free at start, the better any game or intense software will run no matter how affinity timing is managed.
It would be interesting to confirm Core2 is definitely running better with manual affinity management.