Video files loose Transparency

[LucyKosaki]

Not sure if this is an issue with the program or just an export settings issue, but I have some avi videos with transparency (since they are used as transitions) and whenever I use flowframes on it, it seems to loose its transparency. I tried all 4 available codecs for avi export and I tried ProRes mov. As the model I use RIFE 4.0 model which says to support transparency.