My procedure lately is to put in freq/volt, save & apply, power cycle, then system/reboot. I added on the last step after just a power cycle would result in bad stats in Miner Status.
I used to have that issue (and always had to do an SSH reboot after a power cycle). Of late, though, it seems to have been fixed .... all I did once is before I rebooted via SSH, I first went into the System -> Start Up tab and stopped cgminer, then entered reboot in the SSH window. Now the stats are OK after a brutal power cycle .... (but I was called names when I mentioned the stats problem on this forum!)
It doesn't happen every time, but a significant % of power cycles result in Miner Status using the previous elapsed time, so everything gets pushed lower. A warm reboot always results in the correct outcome. This is a funny hobby to have, these things have minds of their own.