I'm using my hard drive in an external enclosure, plugged into another computer, and can only see some of my bookmarks.
I've got my hard drive, from my old computer (running Vista), in an external enclosure, plugged into a replacement computer (running WinXP). I only see some of my bookmarks. Why can't I see them all? Both the old computer and the replacement computer are running Firefox 3.6
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What file or files are you looking at to see your bookmarks?
You can "look" at a bookmarks.html file, but Firefox doesn't use that type of file format any longer for storing bookmarks. You may be looking an an old version of your bookmarks, maybe from Firefox 2, if you were using Firefox that long ago - like 2006- 2007 or 2008 if you stuck with Firefox 2 until the end of that line. Firefox 3 and later use an sqlite database, which can't read as easily as an HTML file; and JSON for bookmark backups, which while it is a text based format, there are no line breaks and trying to read that type of file in an ordinary text program would have it off the screen so far that it would wrap around the room a few times.
If you are looking to recover and be able to use your Firefox "personal data" from that old hard drive, see this:
http://support.mozilla.com/en-US/kb/Recovering+important+data+from+an+old+profile