Multiple Video Streams not synced

Long story short;
I have a track with two video streams or angles. They are the exact same in terms of timecode down to the last frame (it's basically the same video but one stream has a color filter for visual effect).
My problem is this: whenever I switch between the two videos, the second video is not synced with the audio. It seems to be a few seconds off, and I'm hoping to get this issue resolved. The first video stream is synced properly regardless, but it's just the second stream that isn't working properly.
If it makes any difference, I'm using .m2v video format and only one audio stream. Anybody have any ideas?

That's actually exactly how I have it, I just added an extra option so you can, in theory, switch between the two versions on the fly.
In the track viewer both video streams are the exact same length, the only issue is when I switch the video angles. I guess I could just erase the second video stream and avoid the problem altogether (don't want that showing up in my final school project now do I), but I really want to figure this out.

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