You’ve probably tried these already, but here goes:
1. After you’ve imported your PNG sequence, right-click it and choose Interpret Footage > Main… At the top, the alpha should be set to either Straight or Premultiplied. I’m guessing this alpha section is greyed out, meaning AE’s not seeing the alpha.
2. Do you have Photoshop? If you have, open up one of your dodgy PNGs and check the transparency. If Photoshop doesn’t see any transparency or alpha (check both the layers and channels palettes) then the image does not have any and the problem is with the program you used to create the PNG. If it DOES see transparency/alpha, then you could do a batch process in Photoshop to convert all the PNGs to some other format that supports alphas – such as TIFF or PSD.
3. Post one of those dodgy PNGs on here so other people can take a peek and offer more advice.
– Paul