The latest firmware (since Oct 2014) is crap on many levels, but that is a sidenote. For a start, I'd desist from changing voltages on that as the default setting of 0000 seems to find its sweet spot, and to add to that (and as you realised) it seems when you set a voltage with the newer firmware, you consistently loose hashrate and have to restart cgminer to recover it. In my opinion, not worth it! If you have the Oct firmware, reflash your rig (a user also posted one here)

Never come accross the permission denied error on an S3 ... are you logging in via SSH as root?