Story Collector uses the Indesign Text export/import functions. There are problems with the inline graphics, which will disappear after the conversion.
I believe, that the problem is solved with the new conversion from InDesign CS2 and Trados 7.5 over the INX file format.
In the old version (Story Collector) you have to copy each inline graphic from the source file into the translated files.
AFAIR, the documentation strongly encourages the InDesign CS layouter to use linked-in images and graphics, exactly for the reason mentioned here.
As long as you do that, and place the file in the same catalogue during re-import, it's easier for you to re-link the objects.
Maybe of little use now, for a document that has already been layouted?!
But for future jobs, tell me if that helps, or if you still have trouble.