Altium through-hole type, "slot" vs "rectangle", effect on copper pour
I don't know if you fixed the problem by now, but this is my idea of it.

I had the same problem as you today.

You probably set the length of the slot to the width and visa versa.

Lets say, based on the image that the width is 1mm and height 4mm.
In the slot properties you have to provide the Hole Size as width (1mm) and Length as Height (4mm). Then you have to rotate the Hole that it points up (not the size and shape data below that, they can be changed freely). Fixed my problem.