AND there's the overhead of having to switch among 13 different levels. You could fix it by removing some of the allowed frequencies, like this:

#COPY FOR CUSTOMIZATION:
# minimum frequency to use
MINFREQ=125
# maximum frequency to use
MAXFREQ=1000
# list of frequency configurations: each "frequency:volt,dsprate"
FREQS="0:20,90 125:25,90 250:36,180 500:38,360 750:60,430 1000:60,500"
SMARTREFLEX_VDD1=0
SMARTREFLEX_VDD2=0
GOVERNOR=ondemand
UP_THRESHOLD=75
SAMPLING_RATE=300000
IGNORE_NICE_LOAD=0
POWERSAVE_BIAS=0

Also, putting it straight to 125 is a waste of energy IMO... And in case of reboots, allowing bigger voltages use to be a fix.