attachment URL not working right

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Hi guys so im working on a site and im using galleries to display images of products and I was wondering why do some images link like this: http://studioanise.com/?attachment_id=249 and display how I want them too while others link like this http://studioanise.com/furniture/new/rolfbenz_cara_001_large/ while having the exact same setting in the gallery options.

Secondly, I edited the index.php template which should change how pages with links like the second one display however all the changes I make do nothing!

Thanks!