This problem might be related to the way it makes decisions on what planets need population. Since the AI has no sense of 'proportion' it will suck a planet dry & send the transport off to the far corners of the known universe. But every so often it must 're-assess' what planets need population. If the transports are still loaded then it probably sees that original world empty and decides to 'move some population' to it.
I have to admit that I haven't seen it act that way myself.
The frustrating thing I've always seen is that it will load a transport full of population and LEAVE IT SITTING THERE. So, you don't get the production bonuses or the additional growth that population would provide ANYWHERE. I've given up on using the population minister in SE IV though I used to use it in SE III. Unfortunately, the AI is stuck with ... the AI! So, I've modded my AIs to limit the size of their population transports and not build too many. This reduces the bad side effects of AI stupidity considerably.