Here's a test with the PMDG 747, at default YBBN ( Gate 78 ), in FSX:SE. Everything's normal.
One thing I've noticed, you have a much higher frame rate than I have (I was at about 45 fps).
Simconnect related to animations happens at each frame, and developers cannot choose the update frequency with much flexibility, it's either every 4 seconds, every second, 6 times per second, or every frame so, in order to have smooth animations, we don't have any choice other than working at every frame, otherwise animations at 6 fps would look very bad.
Now, with your very high frame rate, it's *possible* you are putting too much strain on Simconnect so, all your apps that use it (which includes GSX, but also every other installed app, like SODE, FSUIPC, etc.), will be *forced* to talk with the sim at 100+ fps, all of them.
Try to *limit* your frame rate, and see if this makes a difference. Our animations are made at 30 fps so, anything higher, it's just overkill and you won't see any difference.
We don't have this problem in P3D V4 anymore, since we don't subscribe to Simconnect visual frame events anymore, but we use a more "native" and "low level" API, called PDK, which skips Simconnect for this feature, so we put less strain on the sim in P3D V4. But in FSX, there are no alternatives.