Did you flash the fix he posted in the "ROM Fixes" folder? This fixed the Apps optimizing on every boot for me.
I had the same issue. Every boot 8 apps were optimized.
Then I flashed the fix, wiped C.&D. and next bootup 319 Apps got optimize...
Just upgraded to v6. I can't find USB mass media mode anymore...
- I can't finde the mass media mode in settings
- Turning it on with toggle switch leads to USB device which is not functional
If you don't care about data, just delete everything except /system, and than flash v1.3.0 (I did it that way and it worked just fine), data is suggested to wipe when going from KK for better experience, if you don't delete it, it's not ROM's faul...