Ok, I do not know if this is anything substancial, and I'm only speculating:
Jake worked with Arvin Sloane at SD-6 knowing very well that it was an internation crime syndicate. And I always wondered if "You went behind my back and recruited my daughter." get-up was just a load of horse felgercarb.
This is only speculation, but Jack making Sydney an "Enemy of the State" is proving to be compramising Jack's "good guy" position.
But the more I think about it, it doesn't make any sense. Both Jack and Sydney are agents for the USA and the information was on that funky paper. Why would the US Intelligence Agencies knowinly let persons of major threat go parading through their organizations? It doesn't add up and I think that Jack programing Sydney to be an "Enemy of the State" is either bull felgercarb, or their talking about "Enemy of the State" in means of the State of Bad Guy's International. The later I highly doubt.
What you y'all think?
-Kat