The protected function messages are warnings, not errors, and rarely if ever actually impact game play. That said, it is known the nUI5 has issues with some of the secure code changes that have occurred in WoW over the last couple patches.
Anyway, as noted, they are warnings and not errors and don't usually impact game play. My suggestion would be to just turn off the option in Swatter to report warnings.
Also, there is already a function built into WoW to record taint errors... '/taintlog 0' '/taintlog 1' and '/taintlog 2' I believe are the commands. They write the output to [ World of Warcraft > Logs > taintlog.txt ]
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