I did changes on mine (rooted stock) manually, however the instructions I found had 2 new lines:
<permission name="android.permission.WRITE_EXTERNAL_STORAGE" >
<group gid="sdcard_r" />
<group gid="sdcard_rw" />
<group gid="media_rw"/>
</permission>

and

<permission name="android.permission.WRITE_MEDIA_STORAGE" >
<group gid="sdcard_rw" />
<group gid="media_rw" />
</permission>

It works as it should so far.

Are you running custom ROM or something? maybe that's the problem, because it sounds weird.
Blame Google for this mess, I send them angry e-mail, probably waste of time, but if everybody complains maybe they listen.
But what do you expect from company touting improved performance of their newest KK OS when running in 512 MB RAM, as major selling point, does anybody still makes phones with 512 MB RAM?