I was able to come up with a fix for migrating bookmarks and some other settings (not sure of the entirety of them) from one version to another for Firefox. I'm updating from version 13 to 14 using TA 4.72 on a Win7 capture machine; using a WinXP capture machine also works.
After capturing your Firefox install, the profile that was created when installing Firefox is saved in the package folder in %AppData%\Mozilla\Firefox\Profiles and it is named "random 8 character string".default. Also, if you open the profiles.ini file in %AppData%\Mozilla\Firefox you will see the Path=Profiles/"random 8 character string".default. In order to make the migration work the Sandbox Name in the new version MUST be the same as the old version. However, the Inventory Names can be different.
Go to %AppData%\Mozilla\Firefox\Profiles in your old version and find out what the random 8 character profile name is, lets say it's a1b2c3d4. Now go to your new version package and change whatever the new version "random 8 character string" is to a1b2c3d4. Change it in the "folder".default AND in the profiles.ini file.
Rebuild and deploy your new package and you should be good. The one issue that I have found with this is that if some of your settings are different, i.e. in the old version you had "check for updates" and in the new version you have "never check for updates", the setting will not get overwritten, so Firefox will still check for updates. So in your initial package make sure all the settings are exactly how you want them before you deploy it.
