Due to the inability to use HDMI on the 4.2.2 builds, I jump on the stock ROM (4.1.2) so I can watch netflix on my TV. I've noticed however that when I go back to the slot-2 Avaitor AOKP rom, several things are 'off'
As you recommend, I boot into safestrap, wipe cache/dalvik and fix permissions. This seems to solve most of the quirky problems I encounter, but one thing I've noticed is some apps seem to lose their data...
I've used the built in tweak to configure the external SD card to be seen as internal storage (when I initially setup the rom). A few of the apps I've been experiencing issues with on a regular basis are:
OBackup (seems to 'forget' my device and frequently reports that it is not rooted) - I've deleted it's SU permissions, uninstalled/reinstalled, etc. Seems to get it working again, but still winds up forgetting everything.
XPrivacy will report that it's not enabled in the xposed framework, but when you check xposed, it is in fact enabled (reboot, fix permissions fixes this). But this seems to happen every time I come back from stock slot
Swype Keyboard - This app seems to completely disappear from the system altogether (leaving it's /data/data directory in tact). Rebooting, wipe cache/dalvik and fix permissions does not fix this one. And simply reinstalling the app doesn't work either (an error code is generated when the phone tries to perform the installation.) I then have to delete the com.swype data from the /data/data directory and then reinstall again...
These issues aren't critical or anything, overall I'm a huge fan of the rom and all it's tweaks. Just wondering if anyone else experiences similar issues or knows of any fixes?