It is a glitch that hasn't been addressed yet. http://forum.pfsense.org/index.php/topic,40428.0.html
I have also had that problem on the re-syncing of the packages. What you end up having to do is "clear the package install bit" under backup/restore. Then manually reinstall each of the packages after recovering your setup without the package information attached in the xml file.
1. Clear package bit
2. backup configuration (omitting package info)
3. reinstall packages