I've been plagued with this problem on FS9 over the last week or so, Tried all suggestions about setting sensitivity and null zones, re-calibrated numerous times, all without success.
Eventually I did fix the issue by installing the CH Product Manager software ( I use the CH Rudder pedals) and using it to calibrate the toe brakes. The windows game controller calibration did not seem to do the job.
No problem on FSX as I use FSUIPC to calibrate the brakes and it so was able to workaround the problem. Perhaps if Saitek provide calibration software it is worth playing around with that