Favorites? Isn't that a Windows term? It is a good idea to use a service to save
bookmarks. A good one for Firefox is Foxmarks. It can be found in the Add-ons.
It works across platforms and will synchronize your bookmarks as you work.
Clipmarks is another one. When Firefox installs in Linux it may overwrite, but
it is more likely that it just started a new profile and your old bookmarks are
still there.

They will be stored in your home folder in a hidden file. In Nautilus you need
to activate Show Hidden files by going to the Menu under View or by pressing
Ctrl H. Then look for a folder that starts with a dot called .mozilla, then
browse sub-folders looking for firefox. look for profiles that will either be
default or end in default. Your bookmarks are called bookmarks.html. Just open
it to check and then copy it from one profile to the other.

Where are the balloon pop-ups and what do they say? What are you doing when you
see them? Are they in Firefox or every programme? etc.