Perhaps when you brought it into AI it had a clipping that has to be removed.
How was the transparent image made transparent? Was there a background that wasn't completely removed? (you didn't use the magic wand and then feather, did you?)
Are there spot colors involved?
select the trans background in PS and make it into a clipping path. You can then either export the path to AI to use as a clipping path or save it in PS with the path and place it in AI.
There is no need save the clipping path if using CS2 3 or 4 all you
have to do is have a transparent background and bring it in as a psd
or in CS 4 as a tiff ince CS 4 suports transparent tiffs.
The psd might work with CS 1 as well. I do not recall.