[Suicide Junkie]

You have to be careful with colony ships that are too large. If you have too much population, some gets lost in the colonization process. IIRC, the maximum population of the planet's size for a domed colony is all you can drop, even on a breathable planet.

That was fixed in Version 1.42:

11. Fixed - Sometimes when a colonizer would colonize a planet, not all of the population in its cargo would be dropped to the planet.