Video flickering after export

Hey Guys,
I've been using Adobe Premiere Pro ever since CS4 came out and this is the first time that I've came across this particular issue. Up until last week I was still using CS6 on my 2011 Macbook Pro. Three days ago I went and purchased a brand new 2014 15 inch Macbook Pro and downloaded the Premiere Pro CC Trial on it. I was loving everything about CC until I exported my first project. Half of the clips were flickering so I matched each flickering clip to the timeline and noticed that the only clips that were flickering were the clips that I had nested.
This is what I'm experiencing :
https://www.youtube.com/watch?v=vzfOA2WJFXU&feature=youtu.be
I've tried exporting in different formats, but I really want to export in .h264
This may sound stupid, but is it because it's the trial version?
Any help will be greatly appreciated! Thank you!

I talked with customer support. They suggested that the bug is a result of how I encoded the video in VirtualDub. I used Xvid MPEG-4 codec, and the representative suggested I use a format that is generally more compatible such as H.264 or QuickTime Animation (RLE).
I redid the the conversion with VirtualDub, this time using x264. Unfortunately, this simply introduced new issues when I tried to edit the video.
Interestingly enough, the issue shows up in the preview this time.
I don't know why there are still issues. I would try QuickTime Animation, but I don't know of any free software that would let me perform a conversion. Does anyone know why this happens? If not, does anyone know what software I could try to transcode the video?

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