I wonder if the issue has more to do with Dreamcast output than the fact that other video inputs go through THS7353 buffer which probably has better protection. Is there perhaps a large DC offset on Dreamcast RGB lines – not that it should matter in steady state as the signal is AC coupled on cable and before ADC, but could theoretically cause a spike on powerup. Speaking of that, I recall fixing an early version Kuro VGA module which had one channel routed directly to VGA output without going through respective AC coupling cap. Probably unrelated to this issue, but which VGA cables / modules did you use?
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