I was having a problem similar to this with a new Mac Pro using 10.9.3 – Everything worked fine until time to export. The exported footage had occasional lines through it and some frames would flash green at times. It seemed to be related to FPS. Using 23.98 footage and trying to export it as 29.97 wasn’t working. Exporting the sequence at the same FPS as the source footage seemed to fix the problem. Then I just had to convert the final export to 29.97.