H.264 export, randomly missing audio tracks

Came across a strange issue when exporting a 1080p timeline using the H.264 export option. The first export had some strange video flickering issue, but the audio was fine. So I re-exported and switched to CBR instead of 2 pass VBR. On the 2nd export, the footage looked fine but for some reason tracks 3 and 4 which contained background audio, were not in the exported file, just silence. The thing that concerns me is the only encoding option I changed was the bitrate, and going from VBR to CBR, everything else stayed the same in the 2 exports. I have no idea why Premiere would mysteriously drop 2 of my audio tracks. Has this happened to anyone else? This problem has happened to me before, both with the flickering and missing audio. I've tried the usual updating to current version of Premiere, clearing preferences, etc. and still running into this.

I work in Broadcasting and we use Quicktime HD 1080i h264 with no problems. Plus the file sizes are just amazing (Less than 100mg for a 30 seconds)

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