I have my phone rooted and locked with joker's skinny rom. I use bootstrip to flash it. I think it would work on on stock but don't know. Just go into recovery, backup and flash it. If you phone doesn't boot then go into recovery and restore your backup.
I really don't know as I have not seen that at all. What roms are you using? Are you unlocked? I'm on a joker skinny locked. Are you seeing this with any other themes? Can you flash the Quantum rom fine?
Clear out the sd card, internal memory or bite the bullet and delete those system apps from the zip. Possibly even preform a full data wipe.
So after extensive testing, I have found that 0.4.9 installs fine, but no matter what I have tried 0.4.91 constantly FC's multiple core system apps even after doing a complete system wipe. I have tried every possible combination and I get the same result from each. I even redownloaded .91 just to make sure that wasn't the cause.
I am running skinnyrev1 unlocked.
I would love to get the blacked out system menus, any help would be welcome.
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