Unable to copy files from one /data/data/ directory to another (Root)
Android runs in "SELinux" mode. More information here SELinux concepts

This means in addition to the standard linux permissions it also has additional attributes attached.

Running attr -l myfile showed the following Attribute "selinux" has a 38 byte value for myfile

Using /system/bin/ls -alZ you can see the selinux attribute value.

-rwx------ u0_a141  u0_a141           u:object_r:app_data_file:s0 myfile
-rw------- u0_a141  u0_a141           u:object_r:app_data_file:s0:c512,c768 testfile


The file I copied was missing some extra data on the end, c512,c768, I presume this is something like an AppID. 

Running su -c restorecon myfile fixed this and restored the file to the correct attribute value. Ref: Explanation of the chcon command - Post