other then the auto backup solutions are there any that can be done on my computer? the auto once are nice but they do not add what was restored into cydia causing me to reinstall each app just to get cydia updates
you can do this manually with terminal commands but it does essentially the same thing that pkgbackup does. If you want to know how to do it manually you can do it by following this tutorial here or you can follow one this one that uses a mix between pkgbackup manual ssh backups
well I gave you a way to do it completely manually. But just out of curiousity, you backed up all your cydia apps using pkgbackup and then synced your iPhone to iTunes and then updated. After all of this you redownloaded pkgbackup, restored the packages that you previously backed up and nothing happens? Do your packages show up in pkgbackup?