Thanks for all your suggests.
By testing different image size, I found:
When additional image set to 45 x 45, the thumbnail pictures are shown in correct aspect ratio.
Ollie, your example is GREAT ! How do you know? ;-)
Set to 60x60, the thumbnail images will be stretched up, set to 80 x 80, then more up. Cleared all caches, no change.
When set to 30x30, the thumbnail images will be squeezed short in height, right click can see correct size 30x30 in properties.
Products with no 'options' will not be affected by image size setting, all images are shown correctly. I don't know why it's like this. Anyway, I just set to 45x45, this problem is resolved.
Thanks again.