As we are benchmarking not just CPUs but compact integrated platforms, we should take a look at their graphics performance as well. The systems with Intel CPUs feature Nvidia GeForce 9300 graphics whereas the Athlon II X2 250u works with a mainboard which is based on AMD 785G chipset with an integrated Radeon HD 4200 graphics core. The difference in graphics cores may have a profound effect on the performance of these platforms in 3D applications.
As you can see, AMD platform still cannot match Celeron E3400-based one. GeForce 9300 seems to deliver higher 3D performance than Radeon HD 4200, by the way. This is the only explanation of why ION is occasionally faster than Athlon II X2 250u-based platform.