I'm having a hard time picturing this. Can you post the actual Edge file that you're placing?
Edit: If you're using CS6 you place the OAM file. For earlier file you would indeed need to link to the HTML.
In either case if the stage is 1024x768 there shouldn't be an issue.
make sure to set the overflow setting in Edge to "hidden", maybe that helps.
I have the same problem here. The edge stage is 1024*768 the browser preview works perfect. But as soon as I import the .oam file to indesign the composition gets stretched and croped. Overflow is hidden.