Few things you can try. Make a lossless animation(I prefer QT Animation) and then take that into media encoder and render to your final resolution. Encoder does multi-pass encoding so you should get a better final file.
If the first approach also gives you problems another way would be to make a tiff, pict or jpeg sequence. If it comes out okay, great, but if not - you can find the offending frames, locate the spot in the timeline and replace them using "cntl+alt + s".
Perhaps others here might have some insight on why your render is doing that, but I haven't seen that particular issue before.
Johnny Cuevas, Editor
"I have not failed 700 times. I have succeeded in proving that those 700 ways will not work. When I have eliminated the ways that will not work, I will find the way that will work."
---THOMAS EDISON on inventing the light bulb.