I'm assuming if you look at the planets they're harvesting from, they're at 0Ku/+(whatever their resource production rate is). Basically, your ships are making the trip faster than the planet can produce resources, so when the harvester gets there and does it's job, there's not 250 units for it to pick up, so it just grabs whats there and heads back home. If you're harvesting a planet with a stockpile (such as a new outpost in another system), then you should get a full load every time until you drain it's stockpile.