[Grandpa Kim]

The loading problem can occur by getting a double "load" order. When you give a "colonize" order to an empty ship, a load order is included. If you've put in another "load" order you can confuse the AI and it may cancel the remaining orders. Not sure if this happens every time or is sporadic.

IE
You give the following orders:

Load pop. at planet X (a high pop planet)
Move to planety Y (resupply base)
Colonize planet Z

Your order list will read as follows:

Move to X
Load pop.
Move to Y
Load pop.
Move Z
Colonize Z

Your colony ship will arrive a planet Y with a full load of colonists and cannot add more so it cancels the remaining orders.

Two ways to get around this:

Change your order from colonize Z to move to Z. But then you must correct it after passing planet Y.
OR
Transfer 1 pop. from your starting planet.

Kim