Premiere CC, PIP Out of Sync on Export

I have this problem that's been driving me crazy the past few days. I have a basic sequence in my Premiere project that features some picture-in-picture. When viewing it in Premiere, the PIPs are perfectly synced how I want them with the main picture, however on export it is out of sync by a few seconds towards the end (the first few PIPs are perfect, though). I have tried multiple formats with the same result. Even creating a new sequence using that sequence (so that there is only one video and audio track and therefore should not logically be able to be out of sync) has failed. I even tried moving the PIPs that are towards the end earlier and later on the timeline coprresponding to how out of sync they are in the exported file, however that doesn't work either.
I have searched extensively and have not been able to find my problem. Are there any ideas?

UPDATE:
I tried re-editing the entire sequence from scratch in a new project and it still has this problem. It seems as though the picture-in-picture runs more quickly than the main picture while having weird lag spikes. I exported it at 240p and 15 frames per second and the video is perfect (besides looking awful). This seems like an annoying bug that is on Adobe's end having to do with encoding. I will try exporting as different file types and report back.

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