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 rather than the windows one.