Just a quick question as I'm not 100% sure about this.

If I'm running Jinteki - Personal Evolution and my opponant chooses to take a Shi.kyu as an agenda (rather than as net damage) do they take the 1 net damage for stealing an agenda?

Yes.

No. Shi.kyu is not "stolen," it is simply added to the score area. It's worded this way to specifically avoid counting as stealing an agenda for purposes of PE, Currents, etc.

Grimwalker is entirely correct but for the sake of completeness I'd like to add that once it has been added to the score area it is considered an Agenda (for the purpose of Datadealer or Phylotic Entanglement).

****. I have read that card wrong then. No it is then!

So doesn't work with Personal Evolution but does with Phylotic Entaglement. Cool beans.