What is the relation between Fi and Scrapper?

Scrapper seems to like Fi a lot. From the beginning, he's awesome with Fi, and just a total Jerk with Link.

That relation never seems to be explained in the game (as of why does Scrapper seems to know Fi from before)

So what is linking those two together?

There is no relation between Fi and Scrapper prior to them meeting in Skyward Sword. Scrapper just becomes instantly infatuated with Fi when he first meets her.

He probably likes her because of her robot-like speech and emotions. Out-of-game, I bet it was just used as a plot device to provide a reason for Scrapper to help them. But to answer your question, the only link between the two is what we see in the game.