I noticed a lot of people complaining about all their bookmarks missing, the same thing happened to me after i installed ff3.5 (i was left with a blank page) - But, thank goodness its very easy to fix.

Who knows what the heck happened to the FastDial folder, but it seems to be corrupt somehow.

Here's the cure for this strange disease!! :P

1. Delete the corrupt fast dial folder from your bookmark menu. (bookmarks/organize bookmarks/bookmark menu)
2. Uninstall FastDial and restart firefox
3. Quickly fly down to mozilla and re-install FastDial - (then restart ff again)
4. Now you should see a bunch of empty boxes
4. All you deleted bookmarks should be in the 'Unsorted Bookmarks' folder. (bookmarks/organize bookmarks/Unsorted Bookmarks)
5. Just click inside the area where the URLs are, and hit Ctrl+A to select all of them.
6. Drag them into the FastDial folder (just located under the bookmark menu)
7. Open a new tab and all your bookmarks should be back around.

Uptional: If you notice some old bookmarks showing up in your thumbanails, they've probably been in the unsorted bookmarks folder for a while, and you've just copied them into the fastdial folder. So, to get rid of them... you know what to do ;)