I run into the same or similar problem. I found out the following: in case the main product is in the same file as the variant, the import works OK. In case only the variant is updated and the main is not in the .csv file, the product_parent_id is not filled in.
This loads OK:
product_name;product_code;product_type;product_parent_id;char_package;price_value
lekkere wijn;lekkere_wijn;main;;;
;lekkere_wijn_fles;variant;lekkere_wijn;Fles;3.45
This is not OK:
product_name;product_code;product_type;product_parent_id;char_package;price_value
;lekkere_wijn_fles;variant;lekkere_wijn;Fles;3.45
In PhPMyAdmin I can see that the import of the variant is done, but the parent_id is not set.