When you import a sequence in After Effects, you are prompted to specify the alpha channel interpretation. You can choose Ignore, unmatted (unpremultiplied) and premultiplied with alpha.
To change this setting, right click on the sequence the project window and choose Interpret Footage > Main.
There you can change the alpha interpretation.
Hope this helps
Salutations - Cheers
Bernard Lebel
btw: I'm just very curious to know why you ask a question related to Maya and After Effects in an XSI forum...?