This could be a lot of things including the codec of the source video, graphics drivers, cashe problems. There's no way to tell without details about your project, your OS, and the version of AE you are using down to the last decimal point.
Ok, this file was fine. I finished the project on the previous version of CC 15. When i updated to the latest version a few weeks ago this issue arose. I have cuda latest version installed also.
I also updated to El Capitan which might affect this also.