i had the same issue with Iconoclasm. What I did to fix the issue was backup select app data, SMS, voice mail, etc, via Chronus, copied the files off via SSH, and restored the phone to factory settings.
I then rejailbroke the iPhone 4 in this newly restored, fresh state, updated Cydia, then added each app, one at a time, until i had all that i needed, and then re-synced with iTunes. (not restoring from backup). I then restored, via Chronus, my SMS and all other specific app data i needed.
Everything is running fine now
I am thinking that after a bunch of installs, uninstalls, and updates, jailbreak-based apps and utilities will just not play nice.
It is not at all like the Apple AppStore where each app is sand-boxed within it's own little world. You REALLY have to take care of what apps you install via Cydia, and how often you add/remove them.