i literally hate pkgbackup sometimes. it worked for me once maybe 1 or 2 years ago... i didnt install it today.. well, i did, then it messed up, and cydia had 0 sources and 0 installed apps..
i jb 4.3.2 and used pkgbackup, did everything correct... but of course cydia didnt load like you are saying..
i re jb with pwnage again, and what i do is write all my apps and sources in my notes dashboard app. i have about 20 apps/tweaks, it all took about 45 minutes to get everything back to normal. i will not be using pkgbackup again.