My turn to apologise, I meant flight-control set up.... the word flight seems to have taken flight and thus managed to confuse us
My history is very similar to your own. I was running XP 32 Bit when I got the Saitek X-52 Pro. First I got the stick and throttle for a HOTAS set-up (never had a yoke).
A couple of months later I got the pedals for added realism, easier and more precise rudder control and of course the foot brakes.
I must mention that I have never made any profiles, never even programmed anything because at the time there was a bit of confusion at the Saitek Support site -- can't even remember what it was all about. So I postponed and postponed etc.
When, as mentioned earlier I added the pedals, I just plugged them in, didn't do any tweaking, didn't even bother to check the axis and what not in the control panel.
So, out of the box everything worked in harmony - what I did notice was that both the rudder on the stick (twisting motion) and the rudder input from the pedals worked at the same time i.e. I could use either one during the same flight.
I changed my desk and had problems fitting my knees under it, so I unplugged the pedals and put them back in the box for the time being (or so I thought).
Now I am running W7 64Bit on a different machine. I simply connected the stick and throttle (the pedals are still in 'storage') and off I went.
As before, I have never had any problems - but keep in mind that I now am not using pedals and I still haven't configured anything or created profiles.
I recall having a similar problem once for a short time. My aircraft would pull to the right (any aircraft) - on the tarmac and in the air. Then I remembered that the previous day I had been messing with my throttle. There is a thumb slider on the throttle which was pushed half way up. I pushed it back all the way down. Additionally there is a thumb wheel toward the top which I managed to re-center. These two adjustments fixed my problem.
In your case, I really don't know. There is always the possibility that the wiring of the pedals is faulty. I'll give you a couple of links which you probably have already perused but if you haven't you might find something helpful there:
If you can't find a solution to the problem, I wouldn't hesitate and approach the Saitek folks via the support forum perhaps.