For Acrobat, the web browser is a single-document environment. That means, regular links will not open a new browser window (Acrobat does not have much control access of the browser).
You might try to use http URIs for your links, and give the "new window" command as part of the URI, making the browser open a new window. However, such links won't work properly when viewing the document directly within Acrobat/Reader.
Hope this can help.
Max Wyss.