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Well, at least creating corrupt output is certainly not the purpose of an encoder. If you don't have a surprisingly buggy encoder build (which one, x264?), then maybe something in your file system is wrong or your harddisk controller drivers are bugged?! I once had similar issues with nForce4 SATA/RAID drivers, but only when copying huge files fast; video encoders are instead rather slow, regarding writing to disk.
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