I have noticed that with mass storeage on and the USB plugged in. You will not be able to communicate with the internal SD card if you reboot with the USB cable plugged in. As soon as you unplug the USB the media scanner will run and the storage will now show in the storage menu. However Titanium could still not access the card untill I rebooted with the USB unplugged.
I tried the reboot on MTP while the USB is plugged in. Everything worked ok except the phone was not recognized by the computer until I unplugged and replugged the USB. Then it connected right away. I also made the move to AoCP from Jellybam 5.1 and was able to duplicate the issue.
Samsun Galaxy S4 I337. SkyFall 2.0 , TWRP 184.108.40.206.
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Apple Iphone5 ,,,,,,, Scratches,Light leaks,I'm Lost oh my.