I slowed down the footage by 25% then exported a .mov (29.97 fps) from Final Cut Po and imported it into After Effects. Now when I ram preview or completely render the video there are red frames every other frame. Sometimes there are red frames every five seconds, and sometimes its just sporadic. I haven't changed the codec, format or size.
It's probably the source footage codec. What is the source? Is your system up to date? You have not given us anything to go on. You might just as well asked "Why is watermelon?"