OK, this seems stupid...

OK, I have a backup of all my stuff, including the .mozilla hidden directory.

I re-install, but all my bookmarks are gone even after I put in a copy of my old .mozilla directory. Why is that?

Generally speaking to get book marks from one browser to another you have to export them from one, and import them to another. I believe that the option to export and import are under Bookmarks > show all book marks and then from there you can import and export.

But I have the same browser as I did when I saved the .mozilla directory --- am I being really stupid?

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.

Thanks colusix, that's a really good link!