Interesting. Might the effect be due to coffee's acidity? When you drink coffee, the environment in your stomach becomes more acidic, which would (just speculating) make it more effective at destroying/metabolising any mal-folded amino-acid metabolites/proteins (i.e. prions, scary stuff).

Pharmacokinetics does not seem to be particularly well understood currently, but we do seem to be finding it's much more important than we thought. That, and whatever you call the 'study of metabolism' (metabolomics?)...