Yes there was a difference in the schema definitions. I've managed to get rid of the change on this one, but I still have differences being generated for others such as
@ORM\JoinTable(
* name="Category_SubCategory",
* joinColumns={@ORM\JoinColumn(name="category_id", referencedColumnName="id")},
* inverseJoinColumns={@ORM\JoinColumn(name="subcategory_id", referencedColumnName="id")}
* )
where as I only want
@ORM\JoinTable(
* name="Category_SubCategory"
* )
Otherwise the indexes get regenerated with different names