You didn't include a CSV in your post.
I went on your website and looked at your product 62555 where I can see that you indeed have three dropdowns where you only have one characteristic. In the "manage variant" section of that product, only one variant has a size set. The other variants don't. So it's normal that it doesn't display correctly as the variants data is not correct. That means that the problem is in your CSV which is not correct...Or that you're doing something to the product/characteristics after importing them.
I don't know how you're able to have so much problems with the import...everyone else is using it with variants, options, characteristics, etc, and it works for them...