Parent category permalink keeps showing twice when using subcategory?

I come across this problem (http://wordpress.org/support/topic/subcategory-permalink-keeps-adding-parent-category-twice) that was submitted 2 years ago but has been closed unresolved and i can’t seem to find a solution..?

Basically this is an example of my category structure –
Parent Category = making-cakes
Subcategory = sponge
Post Title = Making a Victoria Sponge Cake

So I want the permalink to look like this –
/making-cakes/sponge/making-a-victoria-sponge-cake/

but i’m getting this –
/making-cakes/sponge-making-cakes/making-a-victoria-sponge-cake/

Does anyone know how to stop it from doing this or why the permalink is only doing this to some of my posts?

My permalink structure is /%category%/%postname%/

Thanks