HELP: Green Screen After Encoding

After being hours on my video, in premiere pro, whith a bunch of videos, music and After Effects videos with effects in it,

When i encode my premiere pro video after 1 hour of encoding in HDV 1080, comes with 788mb which is ok and it's 3:24 mins long.

BUT, when i watch the video strangely in the AE effects parts ex: slow motion GREEN screens come on and eat the video, it's all very wierd and i don't

know what to do, help,

Thanks

These appear randomly in some seconds or even appear for 10 seconds