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It's watercooled and never goes above 38 c even under full load
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Well, temps probably aren't the issue then.
But remember that x264 encoding is more demanding than just about anything else you can do, including gaming. Have you taken a look at the CPU usage to see if it spikes right before the 20 min crash?
Regarding BDRB 3907, can you fool it into working by just setting your clock back?
Also, you could try replacing the version of x264 that comes with 4009 with the one that came with 3907, to eliminate one more variable.