I have experienced this same problem. I can confirm that it only happens while flying through clouds and having turbulence. Yesterday I did a re-install of FSX (w/Acceleration) and and added FSUIPC 4.28. Presto! my PMDG 747 goes out of control whenever flying through cloud turbulence. I was not using any FSUIPC with my FSX prior to this install yesterday.
I can also confirm this happens both with, and without ASX sp3.
My first post here - I came to these forums hoping to find a solution to exactly this subject. I hope a solution is found soon. I'm developing an unhealthy complex about clouds. It's not easy driving my jumbo jet through the sky like a sports car trying to avoid the clouds!
Steven