I am still learning the game, but I think I found an explanation for it. Always when I find a new empire, and swap territory maps, half of my freighter fleet gets dispatched because there are cheaper sources for raw materials in any of their systems. (Mostly their capital) Bad thing is, they don't have enough fuel to pass the whole journey, or I don't have a free-trade agreement yet, so they won't refuel at the alien's planets.
Luckily, this problem is only temporary, and after making one flight or something, most of the freighters act normal again.
What do you think about this?
P.S. I don't really know how to upload saved games to that ftp server you were talking about, but I don't feel there's a need, as I still have to learn a lot. :)