select videos file are choppy in Viewer

I can't seem to figure this one out!

I recently began using a DSLR for video production work and am recording audio on the H4n Zoom. The video files are H.264 and the audio is .wav. I use plural eyes to sync audio and then export the timeline to get one cohesive video file for editing. I am exporting the sequences with the same settings as the original files, which are as follows -

Frame Size: 1920x1080

Aspect Ratio: HDTV 1080i (16:9)

Pixel Aspect Ration: Square

Field Dominance: None

Frame Rate: 29.97

Compressor: H.264

Audio: 48kHz, 16-bit, Channel Grouped

Everything has been working wonderfully until recently - (this is the case with two different projects on two different computers) exported .mov files that play smoothly in quicktime are playing back very choppy in the Viewer. Thing is - when I play other files that were exported in exactly the same way, they play back fine in the Viewer. Each of my projects on each of these two computers is playing back one file choppy. I am running one project from the internal hard drive and the other from an external drive connected via firewire.

I have no idea why this is happening!

Any help/ideas would be greatly appreciated. Thank you!