You're not the first person to find that Adobe Reader doesn't always open PDFs within a browser window. The solution is to turn off that feature:
Go to Start > Programs and open Adobe Reader 9.
Then go to Edit > Preferences.
Click to remove the tick alongside 'Display PDF in browser'.
Click 'OK' and close Adobe Reader.
In future, when you click on a PDF link, it will be displayed in a separate window (rather than embedded within a web page) but you won't really notice any great difference (except, of course, that you'll now actually be able to see the document!).
Chris