Just to be 100% sure nothing else is causing weird issues, I would backup everything from your internal storage and external SD card, reformat your SD card, Odin the stock ND8 tar and the latest Philz Touch Recovery, then try to reproduce your problem.
If you can't reproduce it, root the phone (Philz Touch Recovery / Settings /Re-Root), then breakup the apps with data you restore into half. Restore only that half and try to reproduce the problem. Each time the problem doesn't occur, do a nandroid backup and restore another half of what's not restored yet. Once you can reproduce the problem, you'll have narrowed it down.
Once you can reproduce the problem, restore the last nandroid and restore half of what you had previously tried, etc. Keep going until you narrow the problem down to one, or narrow it down enough to make an educated guess from what's left and try just that one and verify that it's the issue.
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Sent from my Sprint Samsung Galaxy SIII on TouchWiz 4.4.2 with Conquest: Singularity v2.2, Ktoonsez' latest kernel and the latest Philz Touch Recovery.