"The Alpha channel system of PPro is non-standard. Bringing in an alpha-channel rendering from 3DS Max shows PPro's alpha interpretation is way off- the blending doesn't make any sense (premultiplied or not, inverted, etc., still wrong)."
Two fixes we found yesterday:
1: Select sequence > Sequence > Sequence Settings - uncheck box "Composite in Linear Color"
2. Effects > Image Control > Gamma Correction - apply this effect to your layer with the alpha channel
Do either of these solve your problem?