It could be anything. The first thing I would try is rendering an image sequence using the render cue instead of rendering a video file. If the image sequence works you can take that into AME and render a video or put it in Premiere Pro and add audio if necessary.
If that does not solve the problem another solution may be to bring your old SWF files into CC Animate (the new Flash Professional) and render them as something else to bring them into AE. If that isn't possible or doesn't work try running a screen capture of the flash file in a browser and render the screen capture to a lossless video format for use in AE. If that doesn't work I would suggest that you use some time remapping and split things up where the problems occur and use still frames to fix the shaking. You didn't give us any workflow details or explain what you are trying to do with the SWF files so some other more obvious solution may be possible.
Thank you Rick for the answer.
For more information about at I´m doing, is that I animated some texts with In and Out, in the new CC Animated to import that to after effects, instead of doing this inside after effects. The way I solved this problem was by doing the still frame at the moment this start shaking. I will try doing some of solutions you propose. But what intrigues me is way this just happens with some of my swf and not all.