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Hey JJ, I've been seeing your posts pop up here and there now that you've jumped back on the boat.
Anyhow, most of these little quirks are fixed by choosing not to restore your user profile from iTunes after you restore/update your phone to 1.1.4. Rather, set up your phone as new, so that you create a new partnership. Just an FYI, you're not setting your phone up for an extended contract or extending your service, we're just starting a new user profile to sync with.
Anyway, once thats been sorted out, click your Info tab in iTunes and have it sync your contact info and anything else you would have otherwise had migrated automatically during a restore. After that you'll be back to normal, and you'll kiss all those little "quirks" goodbye.
Some thing to consider here is that the User that these applications ran under has changed. It has gone from "root" to the new "mobile" user. As such, some programs still don't work without a little finesse, typically requiring you to change the permissions of a few files to allow for the deprecated "root" user to read/write/modify files now owned by the "mobile" user.
Restoring from a backup after a 1.1.4 jailbreak has shown that many of these deprecated permissions are retained, and as such conflict with the "mobile" user who is now trying to access "root's" restored digital camera folder, email prefs, sound libs, and notes to name a few of the more common problems people have experienced.
My word of advice is to restore to 1.1.4, and then rejailbreak, this time around making sure to set up a New user profile for your phone afterwards rather than restoring the old one.
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