New install and profiles of Fx3b5 on Vista 64.
Importing my Fx2 bookmarks from file (bookmarks.html) using
"Bookmarks > Organize Bookmarks > Import and Backup > Import" results
in the Fx2 "Bookmarks Toolbar Folder" being under the "Bookmarks Menu"
tree, and in Fx3 it's called "Bookmarks Toolbar" without the "Folder".
That's okay.

My Fx2 "Bookmarks Toolbar Folder" contained individual bookmarks,
folders with a mix of individual bookmarks and sub-folders with
bookmarks, and a couple of folders where I'd saved all tabs.

Using Organize Bookmarks (Library), selecting the Fx2 "Bookmarks
Toolbar Folder" under the "Bookmarks Menu" tree in the LHS pane where
they were after importing, selecting all (Ctrl+A) in the RHS pane and
Cut from the context menu, selecting the new Fx3 "Bookmarks Toolbar"
in the LHS pane then Paste from the context menu of the RHS pane,
results in no bookmarks from the sub-folders of folders on the
Bookmarks Toolbar. It's reproducible here. Selecting all and using
drag and drop or "Organize > Move" works okay without the bookmarks
missing from sub-folders. There is no "Move" on the context menu.

In Fx3b5 "Bookmark all tabs" (in a folder) to the "Bookmarks Toolbar"
silently fails if the "Show all the bookmarks folders" drop-down
button is used to expand on the "Bookmark All Tabs dialog.

Also tried the above in a new Fx3b5 profile and no extensions.

I don't know and didn't look if they are known issues, but tried to
figure out what the problem was and find workarounds that WFM.

--
Rom