Have you tried reformatting the persist partition and recreatting all files and folders as described in the guide?
e2fsck 1.42.9 (28-Dec-2013) Superblock has an invalid journal (inode 8). Clear<y>? y yes *** ext3 journal has been deleted - filesystem is now ext2 only *** Superblock has_journal flag is clear, but a journal inode is present. Clear<y>? yes /dev/block/platform/msm_sdcc.1/by-name/persist was not cleanly unmounted, check forced. Pass 1: Checking inodes, blocks, and sizes Journal inode is not in use, but contains data. Clear<y>? yes Pass 2: Checking directory structure Pass 3: Checking directory connectivity Pass 4: Checking reference counts Pass 5: Checking group summary information Block bitmap differences: -(75--1098) Fix<y>? yes Free blocks count wrong for group #0 (2972, counted=3996). Fix<y>? yes Free blocks count wrong (2972, counted=3996). Fix<y>? yes Recreate journal<y>? yes Creating journal (1024 blocks): Done. *** journal has been re-created - filesystem is now ext3 again *** /dev/block/platform/msm_sdcc.1/by-name/persist: ***** FILE SYSTEM WAS MODIFIED ***** /dev/block/platform/msm_sdcc.1/by-name/persist: 30/1024 files (3.3% non-contiguous), 1124/4096 blocks