Here is the scenario:

I have a Komainu on Archives and a Chum in the second layer of ice. Runner plays Parasite on Komainu. Runs and does not break Chum's sub. Continues run and kills Komainu with Datasucker. Chum falls to the first layer and runner encounters it again.

On jinteki.net how it played out was the runner used one datasucker token to kill Komainu (killed it before Chum could give it +2 strength) and now the first Chum sub applies to itself when the runner encounters it again. Runner had 2 cards in hand and flatined. Seem kosher or did jinteki.net bug out on this one?

Jinteki.net bugged out. When you pass the first ice and destroy the second, you do not skip backward to encounter the outermost ice again. It's a known issue if ice is thrown into the trash before the runner passes it.

However, if the ice passed was Chum and you didn't break it, it's not a conditional When Encountered ability, it's a constant ability--that subsequent ice has +2 STR already when you encounter it. You can't kill it before it gains the bonus. And, assuming you were able to (with more Datasucker tokens), when the encounter with that ice ends without all its subroutines being broken, Chum will inflict its damage.

And, even with all *that* said, Datasucker's ability is not a "When Encountered" ability; it's not even that fast. It specifies "Rezzed piece of ice currently being encountered ," so your opportunity to burn down the ice STR is after all When Encountered conditionals have resolved anyway.