Well, actually this was a bug on eBay
You can find more information on eBay developers forum, questions/3635/bug-trading-api-when-shippingttypefreightflat-inte.html#answer-5652
And after following up for several months with eBay support, just two months ago, the bug was fixed, and I was able to programatically push all listings to support international shipping with the Trading API.
Hope this helps to someone having the same problem.