An swf file opened in a browser will size itself to fit the browser while retaining its normal porportions... meaning one dimension of it (height or width) will stretch the full distance of the window. If you want to control the size that the file appears as, you need to embed the file in an html web page. If you select the option to publish an html web page in the Publish Settings, it will automatically create the code that will embed the swf file in a web page at the intended dimensions.
Yes, I know it, but the problem is that Google has indexed
my site as index.swf and not index.html, like I have published...
Googe has indexed the swf of your site, but they are likely to also index your site at some point, though I have no idea of how that show gets managed. In any case, you cannot control how an swf file is displayed in a browser window outside of an html page.