I am using the following headers, which I believe are fine:
sku|attribute_set|type|super_attribute_pricing|simple_skus|configurable_attributes|var_sku
test11|Medlinev01|simple||||1
testconf11|Medlinev01|configurable|test11,test22,test33|var_sku||
The issue, I believe, relies on the fact that Magento tries to add already linked products, so when I manually go into the configurable product menu, within the associated products tab, and hit the reset button they appear to work just fine.
However, when I try to associate them directly from the Magmi file, they dont work. The products are all created (both the simple and the configurable).