if it was a case whereby you purchased a Jetsaver fare, upgraded at check in to starclass and then received points according to j class, it would've been done in error.
As some one who works for ff, the general rule is that technically check in staff for jq are required to advise that if you pay to upgrade at check in, you'll only be awarded points as per your original booking class. This is also suppose to be imprinted on the payment slip as well. eg. You pay for a jetsaver fare and upgrade, you'll be awarded points as per original booking class. Which means you'll receive nothing. If you originally book in a Jetflex fare such as Y class and you pay to upgrade at check in, you earn economy base points.