Problem 1 (no fix known)
Reboot while phone is in sleepmode (press power button to get to lock screen, press it 1nce to turn screen off)
-reboots
-on boot it will optimize all apps, I have 116 apps, takes 10 minutes.
-does not optimize apps on normal reboot.
-seems to be a global cm12.1 problem, someone changed kernals and fixed it. (Googled, its 1 of the top links).
This could take like 30+ minutes if you have a lot of apps.
Problem 2
Internet radios not working..
-no sound
-track displays playing first 1-10 secs
Fix
Install viper4android (requires root access)(sound driver).
Apparently this cm12 sound driver doesn't work with internet radio.
Fix found by dronic
http://androidforums.com/threads/cm-mod-constant-reboots.933708/#post-7043841
Problem 3
Loss of root access after install
-no root access
Fix
-flash latest supersu, the same way you flashed cyanogeod12.
Or
-easier option, go to settings>about phone>build #. Tap build # 7x, this will enable the hidden menu developer options. Settings>developer tools> enable root.