This is not a flaw it is a characteristic of the compination of CPU/OS/Application.
Think of the CPU's as circular highway. Where cars once in their lane cannot change lanes and overtake, unless told to.
The Intel chip has 4 low speed lanes (really two wide lanes that can fit two small cars side by side at a push)
The AMD has just two high speed lanes.
Controlling the traffic slow is a stupid controller, who only sees the lanes and does not take into account traffic flow.
The processes are cars, each with different characteristics, Three of them smaller cars, one a large cumberson car that takes a long time to break and accelerate, but can carry more passengers.
So which highway can carry the most people at any one time?
On the intel highway 4 cars can travell at the same time at a slow speed with little or no influence on each other, the traffic controller does not need to do much, he pushes each car onto it's own lane.
Now the AMD road only has two lanes but capable of very fast speeds, three of the cars can travel at great speed, now the controller can only allow one car per lane so he has to schedual the traffic, he lets two go (fast small cars) that travel great distance in a short space of time in one lane, they then have to stop and allow the other two cars to go. One car can stop and accelerate quickly, once the controller allows the other two to go again, however the large cumberson car has to slow down slowly, before it stops, when it's time to go again it has to accelerate slowly away.
A different controller (say UNIX, or even better an OS/390) controller, would give the slower car a lane to itself and put the other three cars in one lane, ensuring that the flow of traffic is constant rather than stop and start.
Switch HT off on the intel and you would get exacly the same characteristic.