I have the same problem as reported by you. After 20-30 minutes flying I see very small stutters every second or so, especially noticeable in the outside view.
These stutters become worser and worser and after 1 hour flying it becomes difficult to land the airplane safely. The reported FPS is always (between 30-40 FPS) but sometimes I see the number changing to below 10 for a very short period of time when the large stutters are there.
I have tried to find the cause of this problem. The only flight I did not see it was without a connection to IVAO (are you on IVAO) and without USB head phone.
So maybe the problem can be solved with these two components but this can also be coincidence.
But I see also some other symptoms that can give a clue: when I use the flight recorder of the AXE, a file is written in the flightrecorder directory. I see that each time the problem occurs, thousands of small files are written in this directory. Every few seconds or so a new file is created.
I have also a Saitek controller. I have noticed that at the same moment the flightrecorder files start to get created something goes wrong with the rudder pedals. They still work but when I move one pedal to far the plane doesn't turn anymore.
So maybe the Saitek controller is causing this problem. I have Win 8.1 and joysticks seem to be a problem with FSX and P3D. So now I switched of the controllers in P3D and will be using FSUIPC to do the setup of the controllers. This will be my next test.
Snoopy_belgium