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Logo artwork appears in white box

I am a new user to Adobe CS4 and using the software to create rolling credits in After Effects for HD & film post production.

I import a Word document to In design to work on the fonts and layout, and also import and place the logo files at this stage too.
Then I copy and paste to Illustrator to work on colour and then import to After Effects to make it roll.

In Illustrator I work on the logos separately from the text using the direct selection tool to fix the colour so that I get white letters on a black background when the file is moved to After Effects. In most cases this all works fine and I have also managed to bring colour logos across too.

I have one project where in After Effects three of the colour logos appear (each of them) inside their own white box - just like a white sheet of paper with the colour logo has been dropped onto the black background. These logos in question are .ai files and .psd files.

I have other logos in the project of the same file type that work fine so I am wondering if I should do something to the problem logos before placing them.

Any advice on how to remove the 'white sheet of paper' and just leave the colour logo on a black background in After Effects would be appreciated.
I have only taught myself this process and know nothing else about what the software does, so please be gentle and not too technical if anyone is kind enough to reply.