did you export to MOV using the anamiation compression and the millions + color space? the + is the alpha channel, if it isn’t selected there is no alpha channel. Also, make sure there literally is a transparent backgroud by closing the ‘eye’ on any underlying track. I usually select the checkerboard for transparency to make sure there is a transparent background before I ever start. These settings always work for my premiere station. For my Liquid edition editing suite I use the TGA seqence which will work no matter what (in any NLE i’ve ever used).
Good luck…