Whenever you install mozilla/firefox, it creates a sub-directory with a random name for each profile. Be sure you're using the profile matching the backup directory: to do this, go to Help --> Troubleshooting Information and click open containing folder in the Application Basics section. You will discover if your default profile matches the copied directory or not.
In any case, exporting bookmarks from the Organize Bookmarks manager is always advisable, as suggested above. You might keep a backup of the bookmarks in html format, suitable to be imported into any other browser, if needed.
Here is some useful information about managing profiles in Firefox: http://support.mozilla.com/en-US/kb/Managing-profiles
. Hope this helps.