Hi,
I have the same problem with PMDG 747, FSUIPC and ASX. When I get into a turbulence, my aircraft just swings to one side and the autopilot does not react on it (when I try to level it with a yoke, the autopilot disconnects and I get an error message "Extensive column *something*, I do not remember exactly). In that case I have to fly the aircraft manually as long as the turbulence occurs and when it is gone I can connect the autopilot again (and it puts the airplane back to LNAV path).
I am using:
FSX w. Acceleration Pack
PMDG 747 w. SP 2.1
FSUIPC 4.28 (wind smoothing enabled)
ASX w. SP3 (wind smoothing and stabilization disabled)