Just because other people were talking about this. My two cents worth:
I think the writers and producers of Smallville are well aware that they have made Lex's possible mutant healing factor ambiguous, and have simultaneously raised both his awareness of this and the apparent malaria alluded to in only the previous episode. I think the ambiguity is quite deliberate.
I think also that Lex's healing power simply makes him heal faster than a normal person, it doesn't entirely protect him from injury or disease. He gets hit on the head; he had an abrasion and a headache; he gets better soon. He gets malaria; he recovers when someone else might have died of the disease or starvation.
Or maybe he never had malaria; his delusions and hallucinations on the island were simply the cumulative effect of all those times he was hit over the head through two seasons.
And who knows what hallucinogenic drugs Helen put have put in his drink?